Modulation of expression of acyltransferases to modify hydroxycinnamic acid content

ABSTRACT

The invention provides methods of engineering plants to modulate hydroxycinnamic acid content. The invention additionally provides compositions and methods comprising such plants.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of PCT/US2013/077266, filed Dec. 20, 2013, which claims benefit of priority of U.S. provisional application no. 61/745,247, filed Dec. 21, 2012, each of which applications is herein incorporated by reference for all purposes.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

This invention was made with government support under Contract No. DE-ACO2-05CH11231 awarded by the U.S. Department of Energy. The government has certain rights in this invention.

REFERENCE TO SUBMISSION OF A SEQUENCE LISTING

This application includes a Sequence Listing as a text file named “77429-948215_SEQ” created Jun. 18, 2015 and containing 148,315 bytes. The material contained in this text file is incorporated by reference in its entirety for all purposes.

BACKGROUND OF THE INVENTION

Grasses constitute about 20% of natural land cover (Kellogg, 2001) and the majority of cultivated biomass (57%) that can be sustainably produced in the U.S. (US-DOE, 2011). Rice straw, for example, represents approximately 23% of all agricultural waste, globally (Lal, 2005). The inefficiency of deconstructing cell walls into their component sugars represents a key limitation for production of biofuels from biomass via biological conversion (Lynd et al., 2008). On the other hand, root and leaf litter composition significantly affects soil carbon storage (Zhou et al., 2012). The cell wall components of whole grains also have beneficial effects in human health and various impacts on food processing (Fincher, 2009). For these reasons, grass cell wall properties critically impact unmanaged and managed ecosystems and economic uses.

In contrast to the cell walls of dicotyledenous plants (type I), cell walls of grasses and other Commelinoid monocots (type II) consist of up to 40% dry weight of the polysaccharide xylan, even in primary walls (reviewed in: (Carpita, 1996; Vogel, 2008; Scheller and Ulvskov, 2010)). Grass xylan is substituted with arabinofuranose side chains and infrequently with glucuronic acid (Obel et al., 2006). Of apparent significance to the structure of grass cell walls, ferulic acid (FA, FIG. 1A) esterifies to a fraction of the arabinose sidechains of xylan (reviewed in (Buanafina, 2009)). Dehydrodimers of ferulate (diferulates) form through oxidative coupling likely mediated by peroxidases (Takahama and Oniki, 1994; Bunzel et al., 2008) and cross-link adjacent xylan strands to one another (Ishii, 1991; Allerdings et al., 2005). Furthermore, the observation of ether linkages between ferulate and monolignols suggests that ferulic acid on arabinoxylan may nucleate lignin polymerization (Bunzel et al., 2004). Another hydroxycinnamate, para-coumaric acid (p-CA, FIG. 1A), is also ester-linked to grass cell walls. p-Coumaryl esters are more abundant on lignin, but have also been found to be esterified to grass arabinoxylan (Mueller-Harvey et al., 1986; Ishii et al., 1990; Faulds et al., 2004; Ralph, 2010). Though p-CA is readily oxidized to its radical, p-CA dimers have not been observed (Ralph et al., 1994). Rather p-coumaryl substituents may act as “radical catalysts” rapidly passing the radical to synapyl alcohols and facilitating lignin polymerization (Takahama and Oniki, 1994; Ralph, 2010).

FA on arabinoxylan, and especially diferulates, are thought to act to strengthen primary and secondary cell walls. For example, diferulate accumulation anticorrelates with fescue leaf elongation (MacAdam and Grabber, 2002). Similarly, hydroxycinnamate amounts anticorrelate with rice internode expansion (Sasayama et al., 2011). Cell wall FA content inversely correlates with enzymatic sugar release parameters in vitro (Grabber et al., 1998; Grabber et al., 1998; Lam et al., 2003; Casler and Jung, 2006). In addition, both cell wall-associated diferulates and free and cell wall-associated FA and p-CA deter fungal pathogens and insect pests of grasses (Santiago et al., 2007; Santiago et al., 2008; Lanoue et al., 2009).

Despite their importance, the proteins that incorporate hydroxycinnamates into grass cell walls are not well-characterized. Recently, Mitchell et al. (2007) proposed that a subclade of proteins with the Pfam domain, PF02458, for which transcripts are more abundant in grasses relative to dicots, might incorporate FA into grass walls. PF02458 domain-containing proteins are acyl CoA-dependent acyltransferases present in plants, fungi, and a few bacteria. In plants, these enzymes have been named BAHD acyltransferase, based on the first biochemically characterized family members. They catalyze the addition of an acyl group from the thioester of coenzyme A primarily to oxygen nucleophiles of diverse acceptor molecules in plant secondary metabolism (reviewed in: (D'Auria, 2006)).

There are over 50 BAHD members in most sequenced vascular plants (Table I). The BAHD enzymes group robustly into five clades (D'Auria, 2006), though more recently subclades have been proposed (Tuominen et al., 2011). Several characterized members use hydroxycinnamoyl-CoAs as substrates, including the hydroxycinnamoyl-CoA ω-shikimate/quinate hydroxycinnamoyltransferase (HCT) involved in synthesis of lignin precursors (Hoffmann et al., 2003). Other recent reports have described suberin and cutin feruloyl transferases from Arabidopsis thaliana that act to transfer hydroxycinnamoyl-CoA 03-hydroxy fatty acids acyl acceptors (Molina et al., 2009; Rautengarten et al., 2012). Of importance for the possibility that the BAHD acyltransferase subclade identified by Mitchell, hereafter the “Mitchell clade”, might be involved in arabinoxylan modification, other BAHD enzymes catalyze the addition of esters to sugar acceptors, such as in anthocyanin biosynthesis (Unno et al., 2007). Indeed, Piston et al. found that rice plants simultaneously engineered with reduced expression of four genes from this Glade show a ˜20% reduction in FA in young leaves (Piston et al., 2010). Furthermore, Withers et al. have recently described the biochemical characterization of one of the members of the “Mitchell clade”, PMT or here called OsAT4, which possesses p-coumaryl-CoA:monolignol aclytransferase activity (Withers et al., 2012).

There is a need to increase the digestibility of grass plants. This invention addresses that need.

BRIEF SUMMARY OF THE INVENTION

The invention is based, in part, on the discovery that the “Mitchell clade” of BAHD acyltrasferases is expanded and diverged in grasses relative to dicots and more primitive plants. The invention is further based, in part, on the discovery that mutants in four of these genes have altered cell wall hydroxycinnamate content. Further, manipulating expression of these genes, e.g., overexpression AT10, AT15, AT7, and/or AT5; or decreasing expression of AT 5, increases arabinoxylan-associated ester-linked p-CA while simultaneously decreasing arabinoxylan-associated FA. Thus, in some aspects, the invention provides methods for engineering grass plants to reduce FA content and increase saccharification, recombinant plants produced by such engineering and methods of using the plants for improved biofuel and feed production.

In one aspect, the invention provides a method of engineering a plant to decrease the ferulic acid content in a plant, the method comprising: introducing an expression cassette into the plant, wherein the expression cassette comprises a polynucleotide encoding an AT10, AT7, AT15, or AT5 acyltransferase wherein the acyltransferase has at least 70% identity to a sequence selected from SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, or SEQ ID NO:8, and culturing the plant under conditions in which the acyltransferase is expressed. In some embodiments, the polynucleotide is operably linked to a promoter endogenous to the plant. In some embodiments, the expression cassette comprises a promoter to which the polynucleotide is operably linked. In some embodiments, the promoter is a tissue-specific promoter, e.g., a promoter that drives expression in cell wall. In some embodiments, the polynucleotide has at least 70% identity to SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, or SEQ ID NO:7.

In a further aspect, the invention provides a method of engineering a plant to decrease the ferulic acid content in a plant, the method comprising: modifying the plant to decrease expression of an AT5 polypeptide having at least 70% identity to SEQ ID NO:8.

In an additional aspect, the invention provides a grass plant, e.g., rice, corn, switchgrass, sorghum, millet, miscanthus, sugarcane, alfalfa, wheat, soy, rye, barley, turfgrass, hemp, bamboo, rape, sunflower, or brachypodium, genetically modified to over express AT10 AT15, AT7, and/or AT5. In some embodiments, a plant engineered in accordance with the invention, or progeny of said plant, comprises a polynucleotide encoding an AT10, AT15, AT7, or AT5 operably linked to a heterologous promoter. In some embodiments, the plant comprises a heterologous polynucleotide encoding an AT10, AT15, AT7, or AT5 protein.

In another aspect, the invention provides a plant, e.g., a grass plant, comprising a polynucleotide AT5 inhibitor that inhibits expression of a gene encoding AT5.

In a further aspect, the invention provides biomass comprising a plant or a part of a plant genetically modified as described herein to overexpress AT10, AT15, AT7, or AT5; or to disrupt AT5 expression. The invention additionally provides a method of obtaining an increased amount of soluble sugars from a plant in a saccharification reaction, the method comprising subjecting the plant biomass a saccharification reaction, thereby increasing the amount of soluble sugars that can be obtained from the plant as compared to a wild-type plant

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1B. (FIG. 1A) Structures of relevant hydroxycinnamic acids. (FIG. 1B) Inferred Bayesian phylogeny of the rice “Mitchell Clade” BAHD acyl CoA-utilizing enzymes that includes the following: the rice acyltransferases (OsAT); the Arabidopsis gene, AT3G62160, that allowed this Glade to be identified by Mitchell (2007); biochemically characterized BAHD-IV and BAHD-III proteins as an outgroup (ACT and VAAT, refs); Arabidopsis proteins that use hydroxycinnamoyl-CoA adducts (HCT and SFT) as substrates; and the rice genes that cluster with the Arabidopsis HCT (HCT-like). Proteins are identified by the locus ID that encodes them or their Genbank ID, followed by their designated abbreviations. Clade credibility values are 100 unless shown. The two major acyltransferase groups are designated Glade i and ii. Color intensity of the circles indicates the level of RNA expression in terms of counts of Sanger ESTs and representation in massively parallel signature sequences (MPSS) data.

FIGS. 2A-2C. Screening results of the cell wall soluble hydroxycinnamate composition of selected T-DNA mutant rice lines. (FIG. 2A) Average ferulic acid content from an alcohol insoluble residue (AIR) preparation. (FIG. 2B) para-Coumaric acid content from AIR. (FIG. 2C) The ratio of ferulic acid (FA) to p-coumaric acid (p-CA), which is not subject to weighing errors. Error bars indicate standard deviations, 2 to 3 plants for each genotype were measured independently. Data are for homozygous negative segregant plants (solid bars) and homozygous mutant plants (hashed or striped bars). Light grey and cross-hatching indicate values for the leaf blade and dark red and horizontal stripes for the leaf sheath. Each plant line is designated by the repository ID and the putative target gene. The first three samples (2A-20021, 2A-40095, and 4A-03423) are from a side tiller harvested 7-weeks after transplanting to the greenhouse, which can be compared to indicate variation at this stage in hydroxycinnamic acid content. The last two, 1B-00523 and 5A-00394, were harvested 10-weeks after transplanting. A line putatively targeting a rice extosin, 5A-00394, demonstrates that heightened HCA levels are typical in older adult plants relative to younger adult plants.

FIGS. 3A-3B. Genomic positions and gene expression data for OsAT10-D1 activation tagged lines (FIG. 3A) Representation of the portion of the rice chromosomes near the T-DNA insertion sites. Exons are represented by wide bars with the direction of transcription indicated by arrows. The insertion site is represented by the triangle, with the left border, nearest the CaMV 35S transcriptional enhancer elements, represented by ‘L’. cDNA regions targeted for amplification in qPCR are depicted as black bands. ‘RT’ stands for retrotransposon and ‘hypoth.’ indicates hypothetical. OsFBK16 is an F-box and kelch-domain containing protein. (FIG. 3B) Average relative gene expression determined via qPCR shows that among genes within 20 kb of the insertion site only acyltransferase expression is altered significantly in young leaves of homozygous plants with the T-DNA insertion (hashed) compared with negative segregants (solid). The observed minor variations in other nearby genes were not consistent among the 3 biological replicates assayed (not shown). Error bars represent the standard deviation of 3-4 biological replicates. Genes with significantly higher expression (p<0.01, unpaired, 2-tailed, Student's t-test) are marked with an asterisk.

FIGS. 4A-4C. (FIG. 4A) OsAT10-D1 plants (4A-03423.5 progeny) are not significantly different in size compared with the negative segregant, wild type (4A-03423.1 progeny) at senescence, 7 months after planting. (FIG. 4B) dry biomass and (FIG. 4C) whole plant seed at senescence for OsAT10-D1 plants. Grey bars indicate wild type (WW, 4A-03423.1 progeny), and hatched bars indicate mutant (TT, 4A-03423.5 and 4A-03423.12 progeny). N=12. Error bars represent 2*SEM. ‘*’ indicates significant differences at p<0.05 (unpaired, 2-tailed, Student's t-test).

FIGS. 5A-5D. OsAT10-D1 shows alterations in cell wall hydroxycinnamic acids. Data are for a negative segregant family lacking the insert (grey bars, progeny of 4A-03423.1) and two mutant families homozygous for the insert (cross hatched bars, progeny of 4A-03423.5; and horizontal hatched bars, progeny of 4A-03423.12) for young leaves and a pool of mature aerial, vegetative material (i.e., mature straw). AIR is alcohol insoluble residue. dsAIR is destarched alcohol insoluble residue. Error bars are 2*SEM of 3 to 5 biological replicates. * indicates significance via two-tailed, unpaired Student's t-test at p<0.05 and ** indicates significance at p<0.01. (FIG. 5A) Ferulic acid content. (FIG. 5B) p-Coumaric acid content. (FIG. 5C) The ratio of ferulic acid (FA) to p-coumaric acid (p-CA), which is not subject to weighing or extraction efficiency errors. (FIG. 5D) FA dimer amounts and the ratio of FA:FA Dimer for young leaf samples from FIG. 5A-C.

FIGS. 6A-6C. Independent OsAt10 over expression lines (cross-hatch) also show altered ratios of hydroxycinnamic acids (HCA) relative to wild-type lines (solid). (FIG. 6A) qRT-PCR shows that primary transgenic (Transg) Ubi::OsAt10 lines 4 and 5 have increased expression of OsAt10 relative to the wild type (WT) Kitaake (Kit) and line 1, which lack the transgene. Relative expression is normalized to the average of the results with WT plants. (FIG. 6B) Hydroxycinnamic acid (i.e., ferulic acid, p-coumaric acid, and the sum of ferulic acid dimer peaks) content of a young leaf from wild type and primary transgenic plants. (FIG. 6C) FA:p-CA ratio, but not the FA:FA dimer ratio is altered in the OsAt10 over expression lines.

FIGS. 7A-7C. The cell wall alteration in OsAT10-D1 hydroxcinnamates is predominantly in the TFA-soluble fraction. Data are for mature straw from wild type (solid, 4A-03423.5 progeny) and mutant (hatched, 4A-03423.1 progeny). P indicates the pellet and S the supernatant after trifluoroacetate treatment (TFA) or mock (no TFA). The times indicates the minutes of TFA treatment. * indicates significance via unpaired, 2-tailed Student's t-test at p<0.05 and ** indicates significance at p<0.01. (FIG. 7A) Ferulic acid content in AIR. (FIG. 7B) p-Coumaric acid content in AIR. (FIG. 7C) The ratio of ferulic acid to p-coumaric acid.

FIGS. 8A-8C. The modified hydroxycinnamates in OsAT10-D1 are attached to a five-carbon sugar. (FIG. 8A) Liquid chromatography-mass spectrometry shows the total ion abundances in the ethyl acetate extracts for (a) wild type and (b) mutant after 50 mM TFA and 2 M NaOH and (c) wild type and (d) mutant after 50 mM TFA treatment only. Labeled peaks were consistent both with standards, when available, and with mass spectra. trans-Cinnamate was added as an extraction control. (FIG. 8B) The major ion in the mass spectrum for unknown peak 1 is consistent with a para-coumarylated five-carbon sugar. (FIG. 8C) The major ion in the mass spectrum for unknown peak 2 is consistent with a feruloylated five-carbon sugar.

FIGS. 9A-9B. OsAT10-D1 mature straw has increased glucose content relative to wild type (4A-03423.5 progeny vs. 4A-03423.1 progeny, respectively). Wild-type samples are solid and mutant samples are hatched. Grey is from whole tissue, blue is AIR, and maroon is destrached AIR. Error bars show 2*SEM of three replicates. ‘**’ indicates a difference at p<0.01 and ‘*’ at p<0.05 via unpaired, 2-tailed, Student's t-test. (FIG. 9A) Mass analysis shows significant increases in glucose both after trifluoroacetate (TFA) and after additional treatment with sulfuric acid (TFA+H2SO4), as well as with the sum of the two treatments. (FIG. 9B) Analysis of the molecular fraction (mol %) of monomeric sugars released by TFA from various biomass fractions shows significant increases in mutant glucose and concomitant decreases in xylose, arabinose, and other sugars.

FIGS. 10A-10C. Principal component analysis of pyrolysis-molecular beam-mass spectrometry data for 4A-03423 corroborate the change in extractable phenolics, but show no difference in lignin composition. (FIG. 10A) First two components for total biomass (negative in PC1) and AIR (positive in PC1) for 4A-03423.1 pool (WT, diamonds and squares) and 4A-03423.1 pool (Mutant, triangles and X's). (FIG. 10B) Loadings plot for PC2 of A. The mass to charge ratios of the four most differentially identified ions are shown the ions that are overrepresented in mutant tissue are 120 (4-vinyl phenol or 2,3-Dihydrobenzofuran), 91 (fragment of 2,3-Dihydrobenzofuran and most phenols) and 94 (phenol). The ion that is underrepresented in the mutants is 150 (coumaryl alcohol/coniferyl alcohol). (FIG. 10C) For samples consisting of the residue remaining after 2 N NaOH extraction, PCA poorly distinguishes mutant and wild type, indicating that the principle components of variation are extractable and, therefore, cannot be polymeric lignin. Symbols are as in (FIG. 10A).

FIGS. 11A-11C. OsAT10-D1 exhibits increased enzymatic and fungal deconstructability. (FIG. 11A) An enzyme cocktail of cellulase and β-glucosidase releases more sugar from destarched AIR from rice straw of OsAT10-D1 (red diamonds, 4A-03423.5 progeny) than from wild-type AIR (light grey circles, 4A-03423.1 progeny). AIR was pretreated at 100 degrees for one hour at pH 5.5 prior to addition of enzyme. Error bars show the values of the two technical replicates. (FIG. 11B) Penicillium sp. YT02 releases greater amounts of sugar from rice straw of OsAT10-D1 (diamonds, 4A-03423.5 progeny) than from wild type straw (circles, 4A-03423.1 T2 progeny) pretreated via acid-explosion. Grey symbols indicate glucose, red symbols xylose, and while symbols arabinose. Error bars show 2*SEM of five replicate cultures. (FIG. 11C) Xylanase activity (dashed lines, red symbols) in the fungal-straw slurry is enhanced in the presence of the mutant straw (diamonds) relative to the wild type straw (circles); whereas, carboxymethyl cellulase activity (solid lines, grey symbols) is unchanged. IU is nmoles of sugar per minute per mL. Error bars show 2*SEM of five replicate cultures.

FIGS. 12A-12B (Supplemental FIGS. 1A-1B). Inferred Bayesian phylogeny for Glade V BAHD CoA acyltransferases identified from diverse species based on grouping closely with the biochemically characterized proteins that are similar to the “Mitchell clade” of BAHD proteins, namely BanAAT, and the taxol biosynthesis genes. Branch likelihood scores are >95% if not specified. The phylogeny was built using Mr. Bayes3.1.2 with 1.5 X106 generations, until the split frequencies decreased below 0.01. Subclades i and ii, described in the text and Suppl. FIG. 1B, are marked.

FIG. 13 (Supplemental FIG. 2). Quantitative gene expression analysis suggests no change in the expression of other closely related acyltransferases the OsAT10-D1(4A-03423.5, + insert, cross-hatched bars) and negative segregant lines (4A-03423.1,—insert, solid bars). Shown are the average relative expression data for each target gene and related BAHD acyltransferases in young leaves. Error bars are 2*SEM of three to four biological replicates.

FIGS. 14A-14C (Supplemental FIGS. 3A-3C). OsAT10-D1 shows consistent alterations in cell wall hydroxycinnamic acids. Data are for young leaves from progeny of negative segregant (NS) wild-type line (4A-03423.1.9, grey bars) and a line that is homozygous for the insert (4A-03423.5.6, crosshatched bars). The average and error bars indicate 2*SEM for the shown biological young leaf replicates. * indicates significance via Student's t-test at p<0.05 and ** indicates significance at p<0.01. (FIG. 14A) Ferulic acid content in an alcohol insoluble residue (AIR) preparation. (FIG. 14B) p-Coumaric acid content from AIR. (FIG. 14C) The ratio of ferulic acid (FA) to p-coumaric acid (p-CA), which is not subject to weighing or extraction efficiency errors.

FIG. 15 (Supplemental FIG. 4). Sugar analysis confirms that xylose, not glucose, is a major constituent released by the 50 mM TFA treatments.

FIG. 16 (Supplemental FIG. 5). Destarched AIR from OsAT10-D1 mature straw has increased glucose content relative to that of the wild type, but no other significant changes by mass. Wild-type (4A-03423.1 progeny) samples are solid and mutant (4A-03423.5 progeny) samples are hatched. Error bars show 2*SEM of three replicates. ‘*’ indicates a difference at p<0.05 via unpaired, two-tailed Student's t-test. (A) Mass analysis shows significant increases in glucose (Glc), but not xylose (Xyl) and arabinose (Ara). (B) Mass analysis shows no significant changes in galactose (Gal), fucose (Fuc), rhammnose (Rha), galacturonic acid (GalA), or glucuronic acid (GlcA).

FIGS. 17A-17B (Supplemental FIGS. 6A-6B). Thermogravimetric analysis detects no mass difference upon heating between wild-type and mutant mature straw. (FIG. 17A) Example gravimetric traces throughout heating. The first heating phase (red line, right axis) represents heating in the absence of oxygen and the second represents heating in the presence of oxygen (combustion). Data are normalized to values at 30 minutes (177° C.), which represent the initial dry weights. (FIG. 17B) Selected times report on biomass composition. WT and OsAT10-D1 are indistinguishable in terms of the mass of char (blue bars) remaining after pyrolysis at 800° C. (blue bars, t=112′), the ash content after combustion (red bars, t=250′), and, by extension, the fraction of the char that is combustible (yellow bars, difference between char and ash). This provides further evidence that there is no difference in the lignin composition or content between the two genotypes. Switchgrass, oak, and duckweed samples are shown for comparison. Values are % of the dry weight and averages were taken, when replicates were available. When shown, error bars are 2*SEM of 2-4 technical replicates.

FIG. 18 (Supplemental FIG. 7). Enzymatic activity in media during Penicillium sp. YT02 incubation with wild-type (circles) and OsAT10-D1 mutant (diamonds) straw. FPA (dashed lines, red symbols) is the activity on cellulose filter paper. β-glucosidase activity uses cellobiose as a substrate. IU is nmoles of sugar per minute per mL. Data are normalized for mg of total protein. Error bars show 2*SEM of five replicate cultures.

FIGS. 19A-19B. Genomic positions and gene expression data of the OsAT5-D1 activation tagged line. Genomic positions and gene expression data for the OsAT5-D1 activation tagged line (FIG. 19A) Representation of the portion of the rice chromosome near the T-DNA insertion site. Exons are represented by wide bars with the direction of transcription indicated by arrows. The insertion site is represented by the triangle, with the left border, nearest the transcriptional enhancer elements, represented by ‘L’. cDNA Regions targeted for amplification in qPCR are depicted as black bands. RT stands for retrotransposon and hypoth indicates hypothetical. (FIG. 19B) Average normalized gene expression determined via qPCR shows that among genes within 20 kbp of the insertion site only acyltransferase expression is altered significantly in young leaves of homozygous plants with the T-DNA insertion (hashed) compared with negative segregants (solid). Error bars represent the standard deviation of 3-4 biological replicates. Genes with significantly higher expression (p<0.01, Student's t-test) are marked with an asterisk.

FIGS. 20A-20D. OsAT5-D1 shows alterations in cell wall hydroxycinnamic acids. Data are for two separately grown batches (#1 and #2) of plants of a near isogenic family lacking the insert (grey bars, progeny of the near isogenic wild type line 2A-20021.10.2) and a family homozygous for the insert (cross-hatched bars, progeny of the OsAT5-D1 mutant line 2A-20021.11.7). Samples for batch #1 were harvested from seedlings 35 days post germination. The expanding leaf samples for batch #2 were harvested at 8 weeks post germination and the mature tiller at 16 weeks post germination. Values are the average of 5 to 12 individual plants. Error bars mark the 95% confidence interval for the mean. * indicates significance via Student's t-test at p<0.05 and ** indicates significance at p<0.01. (FIG. 20A) Ferulic acid content in an alcohol insoluble residue (AIR) preparation. (FIG. 20B) p-Coumaric acid content from AIR. (FIG. 20C) The ratio of ferulic acid (FA) to p-coumaric acid (CA), which is not subject to weighing or extraction efficiency errors. (FIG. 20D) Major FA dimer species and the ratio of FA to dimer for the Batch #1 expanded leaf samples.

FIGS. 21A-21C. Alignment of illustrative AT10 polypeptide sequences. (SEQ ID NOS:2 and 9-15)

FIGS. 22A-22C. Alignment of illustrative AT15 polypeptide sequences. (SEQ ID NOS:16, 17, 4, and 18-22)

FIGS. 23A-23E. Alignment of illustrative AT7 polypeptide sequences. (SEQ ID NOS:23, 24, 6, and 25-32)

FIGS. 24A-24D. Alignment of illustrative AT5 polypeptide sequences. (SEQ ID NOS:33-42)

FIGS. 25A-25B shows the Genomic positions and gene expression data for the OsAT5 activation tagged line. (FIG. 25A) Representation of the portion of the rice chromosomes near the T-DNA insertion sites. Exons are represented by wide bars with the direction of transcription indicated by arrows. The insertion site is represented by the triangle, with the left border, nearest the transcriptional enhancer elements, represented by ‘L’. cDNA Regions targeted for amplification in qPCR are depicted as black bands. RT stands for retrotransposon and hypoth indicates hypothetical. (FIG. 25B) Average normalized gene expression determined via qPCR shows that among genes within 20 kbp of the insertion site only acyltransferase expression is altered significantly in young leaves of homozygous T2 plants with the T-DNA insertion (hashed) compared with negative segregants (solid). The observed minor variations in other nearby genes were not consistent among the 3 biological replicates assayed (not shown). Only 1 of 3 biological replicates for Os05g19920 in the absence of the insert gave a signal distinguishable from background, consistent with that locus' tentative annotation and lack of gene expression evidence. Error bars represent the standard deviation of 3-4 biological replicates. Genes with significantly higher expression (p<0.01, Student's t-test) are marked with an asterisk.

FIGS. 26A-26B illustrates that the cell wall alteration in OsAT5-D1 straw is predominantly to the (50 mM TFA, 100° C.)-insoluble fraction. Wild type samples are (solid) and mutant samples (hatched). P indicates the pellet and S the supernatant after TFA treatment (TFA) or mock (no TFA). The numbers indicate the minutes of TFA treatment. (FIG. 26A) Ferulic acid (FA) content in dsAIR. (FIG. 26B) p-Coumaric acid (pCA) content in dsAIR.

FIG. 27 provides an amino acid sequence alignment between AsFMT (14679; SEQ ID NO:102) and OsAT5 (14681; SEQ ID NO:8) run in NCBI with the CLUSTALW algorithm. Sequence identity is only 18% and similarity is 30%.

FIGS. 28A-28C shows LC/MS spectra of yeast metabolite analyses for (FIG. 28A) authentic coniferyl ferulate, (FIG. 28B) yeast fed with ferulic acid and coniferyl alcohol, and (FIG. 28C) yeast fed with ferulic acid and coumaryl alcohol. The chromatogram correspond to: yeast carrying empty vector (top line); yeast expressing 4CL (2^(nd) line from the top); yeast expressing AT5 (3^(rd) line from the top); and yeast expressing both 4CL and AT5 (bottom line). The MS spectra correspond to the peaks indicated by the arrows.

FIG. 29 provides a table showing a substrate specificity matrix. NA: No activity; ¹Detected product with same retention time as ferulic acid adduct.

DETAILED DESCRIPTION OF THE INVENTION I. Definitions

As used herein, the term “AT10 acyl transferase” refers to a CoA p-coumaryl transferase that functions in the modification of grass arabinoxylan. The term encompasses variants and interspecies homologs to the specific polypeptides described herein. A nucleic acid that encodes an AT10 acyl transferase refers to a gene, pre-mRNA, mRNA, and the like, including nucleic acids encoding polymorphic variants, alleles, mutants, and interspecies homologs of the particular amino acid sequences described herein. Thus, in some embodiments, an At10 acyl transferase gene encodes a polypeptide having an amino acid sequence that has at least 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater, amino acid sequence identity, preferably over a region of at least about 25, 50, 100, 200 or more amino acids, or over the length of the entire polypeptide, to an amino acid sequence of SEQ ID NO:2; or to amino acids 4 to 434 of SEQ ID NO:2; or to any one of the AT10 amino acid sequences shown in FIGS. 21A-21C. Examples of AT 10 genes and the proteins encoded by the genes are shown in FIGS. 21A-21C.

As used herein, the term “AT15 acyl transferase” refers to a CoA feruloyl transferase that functions in the modification of a molecule that effects the amount of ferulic acid incorporated into grass cell wall. The term encompasses variants and interspecies homologs to the specific polypeptides described herein. A nucleic acid that encodes an AT15 acyl transferase refers to a gene, pre-mRNA, mRNA, and the like, including nucleic acids encoding polymorphic variants, alleles, mutants, and interspecies homologs of the particular amino acid sequences described herein. Thus, in some embodiments, an AT15 acyl transferase encodes a polypeptide having an amino acid sequence that has at least 70%, typically at least 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater, amino acid sequence identity, preferably over a region of at least about 25, 50, 100, 200 or more amino acids, or over the length of the entire polypeptide, to an amino acid sequence of SEQ ID NO:4, or to amino acid 5 to 429 of SEQ ID NO:4, or to any one of the AT15 amino acid sequences shown in FIGS. 22A-22C. Examples of AT15 genes and the proteins encoded by the genes are shown in FIGS. 22A-22C.

As used herein, the term “AT7 acyl transferase” refers to a CoA feruloyl transferase that functions in the modification of grass cell walls. The term encompasses variants and interspecies homologs to the specific polypeptides described herein. A nucleic acid that encodes an AT7 acyl transferase refers to a gene, pre-mRNA, mRNA, and the like, including nucleic acids encoding polymorphic variants, alleles, mutants, and interspecies homologs of the particular amino acid sequences described herein. Thus, in some embodiments, an AT7 acyl transferase encodes a polypeptide having an amino acid sequence that has at least 70%, typically at least 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater, amino acid sequence identity, preferably over a region of at least about 25, 50, 100, 200 or more amino acids, or over the length of the entire polypeptide, to an amino acid sequence of SEQ ID NO:6 or to amino acid residues 9 to 439 of SEQ ID NO:6, or to any one of the AT7 amino acid sequences shown in FIGS. 23A-23E. Examples of AT7 genes and the proteins encoded by the genes are shown in FIGS. 23A-23E.

As used herein, the term “AT5 acyl transferase” refers to a CoA feruloyl transferase that functions in the modification of grass cell wall components. The term encompasses variants and interspecies homologs to the specific polypeptides described herein. A nucleic acid that encodes an AT5 acyl transferase refers to a gene, pre-mRNA, mRNA, and the like, including nucleic acids encoding polymorphic variants, alleles, mutants, and interspecies homologs of the particular amino acid sequences described herein. Thus, in some embodiments, an AT7 acyl transferase encodes a polypeptide having an amino acid sequence that has at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater, amino acid sequence identity, preferably over a region of at least about 25, 50, 100, 200 or more amino acids, or over the length of the entire polypeptide, to an amino acid sequence of SEQ ID NO:8, or to amino acids 5 to 429 of SEQ ID NO:8, or to any one of the AT5 amino acid sequences shown in FIGS. 24A-24D. Examples of AT5 genes and the proteins encoded by the genes are shown in FIGS. 24A-24D.

The terms “increased level of activity,” or “increased activity” refer interchangeably to an increase in the amount of activity of an AT10, AT15, AT7, or AT5 acyltransferase protein in a grass plant engineered to increase expression of the acyltransferase compared to the amount of activity in a wild-type (i.e., naturally occurring) plant. In some embodiments, increased activity results from increased expression levels. An increased level of activity or increased level of expression can be an increase in the amount of activity or expression of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% or greater, compared to a wildtype plant. In some embodiments, the increased acyltransferase activity or expression is localized to one or more tissues of the engineered plant, such as cell walls and/or leaves. Increased expression or activity of the acyltransferase gene or protein can be assessed by any number of assays, including, but not limited to, measuring the level of RNA encoded by the AT10, AT15, AT7, or AT5 acyltransferase gene, the level of AT10, AT15, AT7, or AT5 protein, the level of AT10, AT15, AT7, or AT5 enzymatic activity, or by measuring the cell wall ferulic acid and optionally, p-coumaric acid content in comparison to the amount in a wild-type plant.

The terms “reduced level of activity,” “reduced activity” and “decreased activity” refer interchangeably to a reduction in the amount of activity of AT5 protein in a plant engineered to decrease AT5 compared to the amount of activity in a wild-type (i.e., naturally occurring) plant. In some embodiments, reduced activity results from reduced expression levels. A reduced level of activity or a reduced level of expression can be a reduction in the amount of activity or expression of AT5 of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% or greater. In some embodiments, the reduced level of activity or reduced level of expression occurs, throughout all the tissues of the engineered plant. In some embodiments, the reduction in the amount of activity or expression is localized to one or more tissues of the engineered plant, such as the cell wall. In some embodiments, the AT5 is not reduced in amount, but is modified in amino acid sequence so that the enzymatic activity is reduced directly or indirectly. Decreased expression or activity of an AT5 gene or protein can be assessed by any number of assays, including, but not limited to, measuring the level of RNA encoded by the AT5 gene, the level of AT5 protein, the level of AT5 enzymatic activity, or by measuring the cell wall ferulic acid and/or p-coumaric acid content.

The terms “polynucleotide” and “nucleic acid” are used interchangeably and refer to a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5′ to the 3′ end. A nucleic acid of the present invention will generally contain phosphodiester bonds, although in some cases, nucleic acid analogs may be used that may have alternate backbones, comprising, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or O-methylphophoroamidite linkages (see Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press); positive backbones; non-ionic backbones, and non-ribose backbones. Thus, nucleic acids or polynucleotides may also include modified nucleotides that permit correct read-through by a polymerase. “Polynucleotide sequence” or “nucleic acid sequence” includes both the sense and antisense strands of a nucleic acid as either individual single strands or in a duplex. As will be appreciated by those in the art, the depiction of a single strand also defines the sequence of the complementary strand; thus the sequences described herein also provide the complement of the sequence. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. The nucleic acid may be DNA, both genomic and cDNA, RNA or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases, including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine, isoguanine, etc.

The term “substantially identical,” used in the context of two nucleic acids or polypeptides, refers to a sequence that has at least 50% sequence identity with a reference sequence. Percent identity can be any integer from 50% to 100%. Some embodiments include at least: 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, compared to a reference sequence using the programs described herein; preferably BLAST using standard parameters, as described below. For example, an AT10 polypeptide may have a sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to a sequence of SEQ ID NO:2.

Two nucleic acid sequences or polypeptide sequences are said to be “identical” if the sequence of nucleotides or amino acid residues, respectively, in the two sequences is the same when aligned for maximum correspondence as described below. The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. When percentage of sequence identity is used in reference to proteins or peptides, it is recognized that residue positions that are not identical often differ by conservative amino acid substitutions, where amino acids residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated according to, e.g., the algorithm of Meyers & Miller, Computer Applic. Biol. Sci. 4:11-17 (1988) e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif., USA).

For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.

A “comparison window,” as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection.

Algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1990) J. Mol. Biol. 215: 403-410 and Altschul et al. (1977) Nucleic Acids Res. 25: 3389-3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (NCBI) web site. The algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al, supra). These initial neighborhood word hits acts as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a word size (W) of 28, an expectation (E) of 10, M=1, N=−2, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a word size (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).

The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.01, more preferably less than about 10⁻⁵, and most preferably less than about 10⁻²⁰.

Nucleic acid or protein sequences that are substantially identical to a reference sequence include “conservatively modified variants.” With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.

As to amino acid sequences, one of skill will recognize that individual substitutions, in a nucleic acid, peptide, polypeptide, or protein sequence which alters a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art.

The following six groups each contain amino acids that are illustrative conservative substitutions for one another:

1) Alanine (A), Serine (S), Threonine (T);

2) Aspartic acid (D), Glutamic acid (E);

3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

(see, e.g., Creighton, Proteins (1984)).

Another indication that nucleotide sequences are substantially identical is if two molecules hybridize to each other, or a third nucleic acid, under stringent conditions. Stringent conditions are sequence dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Typically, stringent conditions will be those in which the salt concentration is about 0.02 molar at pH 7 and the temperature is at least about 60° C. For example, stringent conditions for hybridization, such as RNA-DNA hybridizations in a blotting technique are those which include at least one wash in 0.2×SSC at 55° C. for 20 minutes, or equivalent conditions.

The term “promoter,” as used herein, refers to a polynucleotide sequence capable of driving transcription of a DNA sequence in a cell. Thus, promoters used in the polynucleotide constructs of the invention include cis- and trans-acting transcriptional control elements and regulatory sequences that are involved in regulating or modulating the timing and/or rate of transcription of a gene. For example, a promoter can be a cis-acting transcriptional control element, including an enhancer, a promoter, a transcription terminator, an origin of replication, a chromosomal integration sequence, 5′ and 3′ untranslated regions, or an intronic sequence, which are involved in transcriptional regulation. These cis-acting sequences typically interact with proteins or other biomolecules to carry out (turn on/off, regulate, modulate, etc.) gene transcription. Promoters are located 5′ to the transcribed gene, and as used herein, include the sequence 5′ from the translation start codon (i.e., including the 5′ untranslated region of the mRNA, typically comprising 100-200 bp). Most often the core promoter sequences lie within 1-2 kb of the translation start site, more often within 1 kbp and often within 500 bp of the translation start site. By convention, the promoter sequence is usually provided as the sequence on the coding strand of the gene it controls. In the context of this application, a promoter is typically referred to by the name of the gene for which it naturally regulates expression. A promoter used in an expression construct of the invention is referred to by the name of the gene. Reference to a promoter by name includes a wildtype, native promoter as well as variants of the promoter that retain the ability to induce expression. Reference to a promoter by name is not restricted to a particular plants species, but also encompasses a promoter from a corresponding gene in other plant species.

A “constitutive promoter” in the context of this invention refers to a promoter that is capable of initiating transcription in nearly all cell types, whereas a “cell type-specific promoter” or “tissue-specific promoter” initiates transcription only in one or a few particular cell types or groups of cells forming a tissue. In some embodiments, a promoter is tissue-specific if the transcription levels initiated by the promoter in the cell wall are at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 50-fold, 100-fold, 500-fold, 1000-fold higher or more as compared to the transcription levels initiated by the promoter in non-cell wall tissues

A polynucleotide is “heterologous” to an organism or a second polynucleotide sequence if it originates from a foreign species, or, if from the same species, is modified from its original form. For example, when a polynucleotide encoding a polypeptide sequence is said to be operably linked to a heterologous promoter, it means that the polynucleotide coding sequence encoding the polypeptide is derived from one species whereas the promoter sequence is derived from another, different species; or, if both are derived from the same species, the coding sequence is not naturally associated with the promoter (e.g., is a genetically engineered coding sequence, e.g., from a different gene in the same species, or an allele from a different ecotype or variety).

The term “operably linked” refers to a functional relationship between two or more polynucleotide (e.g., DNA) segments. Typically, it refers to the functional relationship of a transcriptional regulatory sequence to a transcribed sequence. For example, a promoter or enhancer sequence is operably linked to a DNA or RNA sequence if it stimulates or modulates the transcription of the DNA or RNA sequence in an appropriate host cell or other expression system. Generally, promoter transcriptional regulatory sequences that are operably linked to a transcribed sequence are physically contiguous to the transcribed sequence, i.e., they are cis-acting. However, some transcriptional regulatory sequences, such as enhancers, need not be physically contiguous or located in close proximity to the coding sequences whose transcription they enhance.

The term “expression cassette” or “DNA construct” or “expression construct” refers to a nucleic acid construct that, when introduced into a host cell, results in transcription and/or translation of an RNA or polypeptide, respectively. Antisense or sense constructs that are not or cannot be translated are expressly included by this definition. In the case of both expression of transgenes and suppression of endogenous genes (e.g., by antisense, RNAi, or sense suppression) one of skill will recognize that the inserted polynucleotide sequence need not be identical, but may be only substantially identical to a sequence of the gene from which it was derived. As explained herein, these substantially identical variants are specifically covered by reference to a specific nucleic acid sequence. One example of an expression cassette is a polynucleotide construct that comprises a polynucleotide sequence encoding a AT10 protein operably linked to a heterologous promoter. In some embodiments, an expression cassette comprises a polynucleotide sequence encoding a AT10 protein that is targeted to a position in a plant genome such that expression of the polynucleotide sequence is driven by a promoter that is present in the plant

The term “plant” as used herein can refer to a whole plant or part of a plant, e.g., seeds, and includes plants of a variety of ploidy levels, including aneuploid, polyploid, diploid and haploid. The term “plant part,” as used herein, refers to shoot vegetative organs and/or structures (e.g., leaves, stems and tubers), branches, roots, flowers and floral organs (e.g., bracts, sepals, petals, stamens, carpels, anthers), ovules (including egg and central cells), seed (including zygote, embryo, endosperm, and seed coat), fruit (e.g., the mature ovary), seedlings, and plant tissue (e.g., vascular tissue, ground tissue, and the like), as well as individual plant cells, groups of plant cells (e.g., cultured plant cells), protoplasts, plant extracts, and seeds. The class of plants that can be used in the methods of the invention is generally as broad as the class of higher and lower plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), gymnosperms, ferns, bryophytes, and multicellular algae.

The term “biomass,” as used herein, refers to plant material that is processed to provide a product, e.g., a biofuel such as ethanol, or livestock feed, or a cellulose for paper and pulp industry products. Such plant material can include whole plants, or parts of plants, e.g., stems, leaves, branches, shoots, roots, tubers, and the like.

The term “decreased ferulic acid content” in the context of this invention refers to a decreased amount of ferulic acid present in cell wall or leaf in an engineered plant of the present invention as compared to a wild-type (i.e., naturally occurring) plant. In the current invention, ferulic acid is typically considered to be decreased when the amount of ferulic acid in the cell wall or leaf is decreased by at least 10%, at least 20, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more relative to the amount of the ferulic acid in the cell wall or leaf in a wild-type plant. Ferulic acid content can be assessed using any method known in the art.

The term “decreased ferulic acid content” also encompasses embodiments where the ratio of ferulic acid to p-coumaric acid is decreased relative to a wild type plant. Thus, in some embodiments, the amount of ferulic acid may be the same as a wild-type plant, but relative to the to p-coumaric acid content, may be increased, thus decreasing the ration of ferulic acid to ferulic acid to p-coumaric acid when compared to a wildtype plant. In the current invention, the ratio of ferulic acid to p-coumaric acid is typically considered to be decreased when the ratio in the cell wall or leaf is decreased by at least 10%, at least 20, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more relative to the ratio of the amount of the ferulic acid in the cell wall or leaf in a wild-type plant.

The term “saccharification reaction” refers to a process of converting biomass, usually cellulosic or lignocellulosic biomass, into monomeric sugars, such as glucose and xylose.

The term “soluble sugar” refers to monomeric, dimeric, or trimeric sugar that is produced from the saccharification of biomass.

The term “increased amount,” when referring to an amount of sugar or soluble sugar obtained from an engineered plant of the present invention, refers to an increase in the amount or yield of sugar that is obtained from saccharification of biomass per amount of starting material, in comparison to corresponding biomass from a wild-type (i.e., naturally occurring) plant. In the context of the present invention, “corresponding biomass from a wild-type plant” refers to plant material that is from the same part of the plant as the biomass from a plant engineered to have modified hydroxycinnamic acid levels. As understood in the art, increased amount or increased yield is based upon comparisons of the same amount of corresponding plant material.

The term “conversion reaction,” as used herein, refers to a reaction that converts biomass into a form of bioenergy. Examples of conversion reactions include, but are not limited to, combustion (burning), gasification, pyrolysis, and polysaccharide hydrolysis (enzymatic or chemical).

The term “increased production,” when referring to an amount of bioenergy production obtained from an engineered plant of the present invention, refers to an increased amount of bioenergy that is produced from subjecting biomass from an engineered plant to a conversion reaction (e.g., combustion, gasification, pyrolysis, or polysaccharide hydrolysis) as compared to the amount of bioenergy that is produced from corresponding biomass from a wild-type (i.e., naturally occurring) plant.

II. Introduction

The invention relates to acyltransferases that modify the hydroxycinnamic acid content in grass plant cell walls. These acyltranferases include AT10, AT15, AT7, and AT5. Plants, e.g., grasses, that are modified to overexpress AT10, AT15, and AT7; and/or are modified to decrease expression of AT5 have reduced ferulic acid content and accordingly, provide an increased yield, relative to a wild-type plant, in obtaining sugars from plant wall material. In some embodiments, plants, e.g., grass plants, may be modified to overexpress AT5, resulting in an increase of feruloyl esters. Not to be bound by theory, depending on the cell wall precursor that is modified, increasing the level of feruloyl esters present may introduce relatively easily broken bonds that reduce cell wall recalcitrance. For example, increasing ester linkages within the lignin polymer may improve the solubilization of lignin under mild alkaline conditions compared to native lignin. Accordingly, in this embodiment, increasing ferulic acid content of a plant, such as a grass plan, may provide an increased yield, relative to a wild-type plant in which AT5 is not modified, in obtaining sugars from plant wall material.

Plants can be engineered to overexpress an acyltransferase by genetically modifying a plant to overexpress one or more of AT5, AT10, AT15, or AT7 acyltransferase genes as described herein. In some embodiments, overexpresson is targeted to various tissues, e.g., cell wall and/or leaf, using a tissue-specific promoter. An example of a method for fine-tuning AT5, AT10, AT15, or AT7 expression to increase expression in the cell wall is taught in PCT/US2012/023182, which is incorporated by reference. Similarly, ferulic acid content in a plant, e.g., a grass plant, can be increased by genetically modifying a cell to decrease expression of AT5 as described herein.

In some embodiments, a plant may be genetically modified, to disrupt expression of an endogenous AT10, AT15, AT7, and/or AT5 gene and then further modified to express the AT10, AT15, AT7, and/or AT5 gene in a tissue of interest, e.g., cell wall and/or leaf.

The invention additionally provides methods of generating genetically modified plants that overexpress or have reduced levels of AT10, AT15, AT7, and/or AT5 acyltransferase activity and methods of using such plants, e.g., as biomass for degradation reactions to produce soluble sugars or as forage plants.

As used herein in describing nucleic acids and polypeptides of the invention, an “AT” nucleic acid or polypeptides refers to an AT10, AT15, AT7, or AT5 polynucleotide or polypeptide.

Acyltransferase Nucleic Acid and Polypeptide Sequences

The invention employs various routine recombinant nucleic acid techniques.

Generally, the nomenclature and the laboratory procedures in recombinant DNA technology described below are those well known and commonly employed in the art. Many manuals that provide direction for performing recombinant DNA manipulations are available, e.g., Sambrook & Russell, Molecular Cloning, A Laboratory Manual (3rd Ed, 2001); and Current Protocols in Molecular Biology (Ausubel, et al., John Wiley and Sons, New York, 2009).

AT10

AT10 nucleic acid and polypeptide sequences suitable for use in the invention include AT10 nucleic acid sequences that encode a plant AT10 polypeptide as illustrated by the sequences shown in FIGS. 21A-21C, or a substantially identical variant. Such a substantially identical variant typically has at least 70%, or at least 75%, 80%, 85%, 90%, or 95% identity to SEQ ID NO:2. In some embodiments, the variant has at least 70%, or at least 75%, 80%, 85%, 90%, or 95% identity to an AT10 sequence shown in FIGS. 21A-21C. In some embodiments, a nucleic acid that encodes an AT10 polypeptide of the invention has at least 60%, often at least 70%, or at least 75%, 80%, 85%, or 90% identity to the nucleic acid sequence of SEQ ID NO:1. The Pfam domain of SEQ ID NO:2 corresponds to amino acids 4 to 434 of SEQ ID NO:2. AT10 proteins are additionally characterized by the presence of a motif HXXXD at positions 182-186 of SEQ ID NO:2.

A comparison of AT10 sequences is provided in FIGS. 21A-21C. As shown in FIGS. 21A-21C, there are highly conserved regions of the polypeptide sequences. These conserved sequences are not strictly conserved 100% across the various plant protein sequences. For example, one of skill can obtain a variant by using the sequence alignments to identify residues within the conserved sequences that would be expected to retain AT10 function as well as residues outside of the conserved regions that would be expected to be tolerant to substitution.

AT10 activity can be assessed using any number of assays, including assays that evaluate the hydroxycinnamic acid content of cell wall and/or leaf. AT10 activity can be assessed by increasing the expression of AT10 in plant cells. Examples of assays include, but are not limited to the following illustrative assays. Activity may assayed by creation of a transgenic plant by incorporation into the plant genome of an AT10 gene that is associated with a promoter that increases AT10 expression compared to wild-type levels. Alternatively, transient expression assays, such as through infiltration or dipping of plant cells into an Agrobacterium solution, can be used. For both of these assays the read out is measurement of an increase in the cell wall content of p-coumaryl esters associated with cell wall matrix polysaccharide. For this assay, biomass, or a cell wall extraction thereof, is treated with 2M NaOH. The resulting supernatant, or an extract there of, can be analyzed for changes in hydroxycinnamate content via high performance liquid chromatography with UV absorbance detection or another similar method. Alternatively, an in vitro assay can be used to indicate activity of AT10 in attachment of a hydroxycinnamate (e.g., FA or pCA) onto a 5-carbon sugar. This activity can be measured again via liquid chromatography (LC)-UV detection or LC-mass spectrometry, among others

AT15

AT15 nucleic acid and polypeptide sequences suitable for use in the invention include AT15 nucleic acid sequences that encode a plant AT15 polypeptide as illustrated by the sequences shown in FIGS. 22A-22C, or a substantially identical variant. Such a variant typically has at least 75%, 80%, 85%, 90%, or 95% identity to SEQ ID NO:4. In some embodiments, the variant has at least 75%, 80%, 85%, 90%, or 95% identity to an AT15 sequence shown in FIGS. 22A-22C. In some embodiments, a nucleic acid that encodes an AT15 polypeptide of the invention has at least 60%, often at least 70%, or at least 75%, 80%, 85%, or 90% identity to SEQ ID NO:3. The Pfam domain of SEQ ID NO:4 corresponds to amino acids 5 to 411 of SEQ ID NO:4. AT15 proteins are additionally characterized by the presence of a motif, HXXXD. This motif occurs near position 164 in SEQ ID NO:4.

A comparison of AT15 sequences is provided in FIGS. 22A-22C. As shown in FIGS. 22A-22C, there are highly conserved regions of the polypeptide sequences. These conserved sequences are not strictly conserved 100% across the various plant protein sequences. For example, one of skill can obtain a variant by using the sequence alignments to identify residues within the conserved sequences that would be expected to retain AT15 function as well as residues outside of the conserved regions that would be tolerant to substitution.

AT15 activity can be assessed using any number of assays, including assays that evaluate the hydroxycinnamic acid content of cell wall and/or leaf. Examples of assays include, but are not limited to the following illustrative assays. AT15 activity can be assessed by increasing the expression of AT15 in plant cells. This can be accomplished through creation of a transgenic plant by incorporation into the plant genome of an AT15 gene that is associated with a promoter that increases AT15 expression compared to wild-type levels. Alternatively, transient expression assays, such as through infiltration or dipping of plant cells into an Agrobacterium solution, can be used. For both of these assays the read out is measurement of an decrease in the cell wall content of hydroxycinnamyl esters associated with cell wall matrix polysaccharide. For this assay, biomass, or a cell wall extraction thereof, is treated with 2M NaOH. The resulting supernatant, or an extract thereof, can be analyzed for changes in hydroxycinnamate content via high performance liquid chromatography with UV absorbance detection or another similar method.

AT7

AT7 nucleic acid and polypeptide sequences suitable for use in the invention include AT7 nucleic acid sequences that encode a plant AT7 polypeptide as illustrated by the sequences shown in FIGS. 23A-23E, or a substantially identical variant. Such a variant typically has at least 70%, or at least 75%, 80%, 85%, 90%, or 95% identity to SEQ ID NO:6. In some embodiments, the variant has at least 75%, 80%, 85%, 90% or 95% identity to identity to an AT7 sequence shown in FIGS. 23A-23E. In some embodiments, a nucleic acid that encodes an AT7 polypeptide of the invention has at least 60%, often at least 70%, or at least 75%, 80%, 85%, or 90% identity to SEQ ID NO:5. The Pfam domain of SEQ ID NO:6 corresponds to amino acids 9 to 439 of SEQ ID NO:6. AT7 polypeptides are additionally characterized by the presence of a motif HXXXD. This motif occurs near position 176 in SEQ ID NO:6.

A comparison of AT7 sequences is provided in FIGS. 23A-23E. As shown in FIGS. 23A-23E, there are highly conserved regions of the polypeptide sequences. These conserved sequences are not strictly conserved 100% across the various plant protein sequences. For example, one of skill can obtain a variant by using the sequence alignments to identify residues within the conserved sequences that would be expected to retain AT7 function as well as residues outside of the conserved regions that would be tolerant to substitution.

AT7 activity can be assessed using any number of assays, including assays that evaluate the hydroxycinnamic acid content of cell wall and/or leaf. Examples of assays include, but are not limited to the following illustrative assays. AT7 activity can be assessed by increasing the expression of AT7 in plant cells. This can be accomplished through creation of a transgenic plant by incorporation into the plant genome of an AT7 gene that is associated with a promoter that increases AT7 expression compared to wild-type levels. Alternatively, transient expression assays, such as through infiltration or dipping of plant cells into an Agrobacterium solution, can be used. For both of these assays the read out is measurement of an decrease in the cell wall content of hydroxycinnamyl esters associated with cell wall matrix polysaccharide. For this assay, biomass, or a cell wall extraction thereof, is treated with 2M NaOH. The resulting supernatant, or an extract thereof, can be analyzed for changes in hydroxycinnamate content via high performance liquid chromatography with UV absorbance detection or another similar method.

AT5

AT5 nucleic acid and polypeptide sequences that are targeted for disruption in accordance with the invention include AT5 nucleic acid sequences that encode a plant AT5 polypeptide as illustrated by the sequences shown in FIGS. 24A-24D, or a substantially identical variant. Such a variant typically has at least 60% identity, or at least 65%, 70%, 75%, 80%, 85%, 90%, or 95% identity to SEQ ID NO:8. In some embodiments, the variant has at least 70%, 75%, 80%, 85%, 90% or 95% identity to identity to an AT5 sequence shown in FIGS. 24A-24D. In some embodiments, a nucleic acid that encodes an AT5 polypeptide of the invention has at least 60%, often at least 70%, or at least 75%, 80%, 85%, or 90% identity to SEQ ID NO:7. The Pfam domain of SEQ ID NO:8 corresponds to amino acids 5 to 429 of SEQ ID NO:8. AT5 polypeptides are additionally characterized by the presence of a motif, HXXXD. This motif occurs near position 170 in SEQ ID NO:8.

A comparison of AT5 amino acid sequences is provided in FIGS. 24A-24D. As shown in FIGS. 24A-24D, there are highly conserved regions of the polypeptide sequences. These conserved sequences are not strictly conserved 100% across the various plant protein sequences. For example, one of skill can obtain a nucleic acid encoding a variant polypeptide by using the sequence alignments to identify residues within the conserved sequences that would be expected to retain AT5 function as well as residues outside of the conserved regions that would be tolerant to substitution.

AT5 activity can be assessed using any number of assays, including assays that evaluate the hydroxycinnamic acid content of cell wall and/or leaf. Examples of assays include, but are not limited to the following illustrative assays. AT5 activity can be assessed by increasing the expression of AT5 in plant cells. This can be accomplished through creation of a transgenic plant by incorporation into the plant genome of an AT5 gene that is associated with a promoter that increases AT5 expression compared to wild-type levels. Alternatively, transient expression assays, such as through infiltration or dipping of plant cells into an Agrobacterium solution, can be used. For both of these assays the read out is measurement of an decrease in the cell wall content of hydroxycinnamyl esters associated with cell wall matrix polysaccharide. For this assay, biomass, or a cell wall extraction thereof, is treated with 2M NaOH. The resulting supernatant, or an extract thereof, can be analyzed for changes in hydroxycinnamate content via high performance liquid chromatography with UV absorbance detection or another similar method.

Isolation or generation AT polynucleotide sequences can be accomplished by a number of techniques. Cloning and expression of AT genes in accordance with the invention are generally discussed in the context of AT10 genes. One of skill understands that these techniques can be employed to overexpress AT7, AT15, or AT5 genes. Recombinant expression techniques can also be used to disrupt AT5 expression. In some embodiments, oligonucleotide probes based on the sequences disclosed here can be used to identify the desired polynucleotide in a cDNA or genomic DNA library from a desired plant species. Probes may be used to hybridize with genomic DNA or cDNA sequences to isolate homologous genes in the same or different plant species.

Alternatively, the nucleic acids of interest can be amplified from nucleic acid samples using routine amplification techniques. For instance, PCR may be used to amplify the sequences of the genes directly from mRNA, from cDNA, from genomic libraries or cDNA libraries. PCR and other in vitro amplification methods may also be useful, for example, to clone nucleic acid sequences that code for proteins to be expressed, to make nucleic acids to use as probes for detecting the presence of the desired mRNA in samples, for nucleic acid sequencing, or for other purposes.

Appropriate primers and probes for identifying a AT10 gene from plant cells such as moss or spikemoss, can be generated from comparisons of the sequences provided herein. For a general overview of PCR see PCR Protocols: A Guide to Methods and Applications. (Innis, M, Gelfand, D., Sninsky, J. and White, T., eds.), Academic Press, San Diego (1990).

AT10, AT15, AT7, and AT5 nucleic acid sequences for use in the invention includes genes and gene products identified and characterized by techniques such as hybridization and/or sequence analysis using exemplary nucleic acid sequences, e.g., SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, and SEQ ID NO:7.

Preparation of Recombinant Vectors

To use isolated sequences in the above techniques, recombinant DNA vectors suitable for transformation of plant cells, such as grass crop plant cells, are prepared. Techniques for transformation are well known and described in the technical and scientific literature. For example, a DNA sequence encoding an AT10, AT7, AT15, or AT5 polypeptide (described in further detail below), can be combined with transcriptional and other regulatory sequences which will direct the transcription of the sequence from the gene in the intended cells, e.g., grass or other crop plant cells. In some embodiments, an expression vector that comprises an expression cassette that comprises the AT10, AT7, AT15, or AT5 gene further comprises a promoter operably linked to the AT10, AT7, AT15, or AT5 gene. In other embodiments, a promoter and/or other regulatory elements that direct transcription of the AT10, AT7, AT15, or AT5 gene are endogenous to the plant and an expression cassette comprising the AT10, AT7, AT15, or AT5 gene is introduced, e.g., by homologous recombination, such that the heterologous AT10, AT7, AT15, or AT5 gene is operably linked to an endogenous promoter and is expression driven by the endogenous promoter.

Regulatory sequences include promoters, which may be either constitutive or inducible, or tissue-specific.

In some embodiments, recombinant vectors may be prepared to disrupt gene expression, e.g., AT5 gene expression. For example, such a recombinant vector may encode an RNA that disrupts expression of an endogenous gene. Such embodiments are described in greater detail in the section below relating to engineering of plants to decrease expression of an AT gene of interest.

Tissue-Specific Promoters

In some embodiments, a plant promoter to direct expression of an AT gene, e.g., AT10, AT7, AT15, or AT5 gene. in a specific tissue is employed (tissue-specific promoters). Tissue-specific promoters are transcriptional control elements that are only active in particular cells or tissues at specific times during plant development, such as in vegetative tissues or reproductive tissues.

Examples of tissue-specific promoters under developmental control include promoters that initiate transcription only (or primarily only) in certain tissues, such as vegetative tissues, cell walls, including e.g., roots or leaves. A variety of promoters specifically active in vegetative tissues, such as leaves, stems, roots and tubers are known. For example, promoters controlling patatin, the major storage protein of the potato tuber, can be used (see, e.g., Kim, Plant Mol. Biol. 26:603-615, 1994; Martin, Plant J. 11:53-62, 1997). The ORF 13 promoter from Agrobacterium rhizogenes that exhibits high activity in roots can also be used (Hansen, Mol. Gen. Genet. 254:337-343, 1997). Other useful vegetative tissue-specific promoters include: the tarin promoter of the gene encoding a globulin from a major taro (Colocasia esculenta L. Schott) corm protein family, tarin (Bezerra, Plant Mol. Biol. 28:137-144, 1995); the curculin promoter active during taro corm development (de Castro, Plant Cell 4:1549-1559, 1992) and the promoter for the tobacco root-specific gene TobRB7, whose expression is localized to root meristem and immature central cylinder regions (Yamamoto, Plant Cell 3:371-382, 1991).

Leaf-specific promoters, such as the ribulose biphosphate carboxylase (RBCS) promoters can be used. For example, the tomato RBCS1, RBCS2 and RBCS3A genes are expressed in leaves and light-grown seedlings, only RBCS1 and RBCS2 are expressed in developing tomato fruits (Meier, FEES Lett. 415:91-95, 1997). A ribulose bisphosphate carboxylase promoters expressed almost exclusively in mesophyll cells in leaf blades and leaf sheaths at high levels (e.g., Matsuoka, Plant J. 6:311-319, 1994), can be used. Another leaf-specific promoter is the light harvesting chlorophyll a/b binding protein gene promoter (see, e.g., Shiina, Plant Physiol. 115:477-483, 1997; Casal, Plant Physiol. 116:1533-1538, 1998). The Arabidopsis thaliana myb-related gene promoter (Atmyb5) (Li, et al., FEES Lett. 379:117-121 1996), is leaf-specific. The Atmyb5 promoter is expressed in developing leaf trichomes, stipules, and epidermal cells on the margins of young rosette and cauline leaves, and in immature seeds. Atmyb5 mRNA appears between fertilization and the 16 cell stage of embryo development and persists beyond the heart stage. A leaf promoter identified in maize (e.g., Busk et al., Plant J. 11:1285-1295, 1997) can also be used.

Another class of useful vegetative tissue-specific promoters are meristematic (root tip and shoot apex) promoters. For example, the “SHOOTMERISTEMLESS” and “SCARECROW” promoters, which are active in the developing shoot or root apical meristems, (e.g., Di Laurenzio, et al., Cell 86:423-433, 1996; and, Long, et al., Nature 379:66-69, 1996); can be used. Another useful promoter is that which controls the expression of 3-hydroxy-3-methylglutaryl coenzyme A reductase HMG2 gene, whose expression is restricted to meristematic and floral (secretory zone of the stigma, mature pollen grains, gynoecium vascular tissue, and fertilized ovules) tissues (see, e.g., Enjuto, Plant Cell. 7:517-527, 1995). Also useful are kn1-related genes from maize and other species which show meristem-specific expression, (see, e.g., Granger, Plant Mol. Biol. 31:373-378, 1996; Kerstetter, Plant Cell 6:1877-1887, 1994; Hake, Philos. Trans. R. Soc. Lond. B. Biol. Sci. 350:45-51, 1995). For example, the Arabidopsis thaliana KNAT1 promoter (see, e.g., Lincoln, Plant Cell 6:1859-1876, 1994) can be used.

In some embodiments, the promoter is substantially identical to the native promoter of a promoter that drives expression of a gene involved in secondary wall deposition. Examples of such promoters are promoters from IRX1, IRX3, IRX5, IRX8, IRX9, IRX14, IRX7, IRX10, GAUT13, or GAUT14 genes. Specific expression in fiber cells can be accomplished by using a promoter such as the NST1 promoter and specific expression in vessels can be accomplished by using a promoter such as VND6 or VND7. (See, e.g., PCT/US2012/023182 for illustrative promoter sequences).

One of skill will recognize that a tissue-specific promoter may drive expression of operably linked sequences in tissues other than the target tissue. Thus, as used herein a tissue-specific promoter is one that drives expression preferentially in the target tissue, but may also lead to some expression in other tissues as well.

Constitutive Promoters

A promoter, or an active fragment thereof, can be employed which will direct expression of a nucleic acid encoding a fusion protein of the invention, in all or most transformed cells or tissues, e.g. as those of a regenerated plant. Such promoters are referred to herein as “constitutive” promoters and are active under most environmental conditions and states of development or cell differentiation. Examples of constitutive promoters include those from viruses which infect plants, such as the cauliflower mosaic virus (CaMV) 35S transcription initiation region (see, e.g., Dagless, Arch. Virol. 142:183-191, 1997); the1′- or 2′-promoter derived from T-DNA of Agrobacterium tumefaciens (see, e.g., Mengiste supra (1997); O'Grady, Plant Mol. Biol. 29:99-108, 1995); the promoter of the tobacco mosaic virus; the promoter of Figwort mosaic virus (see, e.g., Maiti, Transgenic Res. 6:143-156, 1997); actin promoters, such as the Arabidopsis actin gene promoter (see, e.g., Huang, Plant Mol. Biol. 33:125-139, 1997); alcohol dehydrogenase (Adh) gene promoters (see, e.g., Millar, Plant Mol. Biol. 31:897-904, 1996); ACT11 from Arabidopsis (Huang et al., Plant Mol. Biol. 33:125-139, 1996), Cat3 from Arabidopsis (GenBank No. U43147, Zhong et al., Mol. Gen. Genet. 251:196-203, 1996), the gene encoding stearoyl-acyl carrier protein desaturase from Brassica napus (Genbank No. X74782, Solocombe et al., Plant Physiol. 104:1167-1176, 1994), GPc1 from maize (GenBank No. X15596, Martinez et al., J. Mol. Biol. 208:551-565, 1989), Gpc2 from maize (GenBank No. U45855, Manjunath et al., Plant Mol. Biol. 33:97-112, 1997), other transcription initiation regions from various plant genes known to those of skill. See also Holtorf, “Comparison of different constitutive and inducible promoters for the overexpression of transgenes in Arabidopsis thaliana,” Plant Mol. Biol. 29:637-646, 1995).

Inducible Promoters

In some embodiments, a plant promoter may direct expression of the nucleic acids under the influence of changing environmental conditions or developmental conditions. Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions, elevated temperature, drought or other environmental stress, or the presence of light. Examples of developmental conditions that may effect transcription by inducible promoters include senescence and embryogenesis. Such promoters are referred to herein as “inducible” promoters. For example, the invention can incorporate drought-specific promoter such as the drought-inducible promoter of maize (Busk et al., Plant J, 11: 1285-95, 1997); or alternatively the cold, drought, and high salt inducible promoter from potato (Kirch Plant Mol. Biol. 33:897-909, 1997).

Suitable promoters responding to biotic or abiotic stress conditions include the pathogen inducible PRP1-gene promoter (Ward et al., Plant. Mol. Biol. 22:361-366, 1993), the heat inducible hsp80-promoter from tomato (U.S. Pat. No. 5,187,267), cold inducible alpha-amylase promoter from potato (PCT Publication No. WO 96/12814) or the wound-inducible pinII-promoter (European Patent No. 375091). For other examples of drought, cold, and salt-inducible promoters, such as the RD29A promoter, see, e.g., Yamaguchi-Shinozalei et al., Mol. Gen. Genet. 236:331-340, 1993 are also known.

Alternatively, plant promoters which are inducible upon exposure to plant hormones, such as auxins, may be used to express an AT10, AT7, AT15, or AT5 gene. For example, the invention can use the auxin-response elements E1 promoter fragment (AuxREs) in the soybean (Glycine max L.) (Liu, Plant Physiol. 115:397-407, 1997); the auxin-responsive Arabidopsis GST6 promoter (also responsive to salicylic acid and hydrogen peroxide) (Chen, Plant J. 10: 955-966, 1996); the auxin-inducible parC promoter from tobacco (Sakai, 37:906-913, 1996); a plant biotin response element (Streit, Mol. Plant Microbe Interact. 10:933-937, 1997); and, the promoter responsive to the stress hormone abscisic acid (Sheen, Science 274:1900-1902, 1996).

Plant promoters inducible upon exposure to chemicals reagents that may be applied to the plant, such as herbicides or antibiotics, are also useful for expressing an AT10, AT7, AT15, or AT5 gene in accordance with the invention. For example, the maize In2-2 promoter, activated by benzenesulfonamide herbicide safeners, can be used (De Veylder, Plant Cell Physiol. 38:568-577, 19997); application of different herbicide safeners induces distinct gene expression patterns, including expression in the root, hydathodes, and the shoot apical meristem. An AT10, AT7, AT15, or AT5 coding sequence can also be under the control of, e.g., a tetracycline-inducible promoter, such as described with transgenic tobacco plants containing the Avena sativa L. (oat) arginine decarboxylase gene (Masgrau, Plant J. 11:465-473, 1997); or, a salicylic acid-responsive element (Stange, Plant J. 11:1315-1324, 1997; Uknes et al., Plant Cell 5:159-169, 1993); Bi et al., Plant J. 8:235-245, 1995).

Examples of useful inducible regulatory elements include copper-inducible regulatory elements (Mett et al., Proc. Natl. Acad. Sci. USA 90:4567-4571, 1993); Furst et al., Cell 55:705-717, 1988); tetracycline and chlor-tetracycline-inducible regulatory elements (Gatz et al., Plant J. 2:397-404, 1992); Roder et al., Mol. Gen. Genet. 243:32-38, 1994); Gatz, Meth. Cell Biol. 50:411-424, 1995); ecdysone inducible regulatory elements (Christopherson et al., Proc. Natl. Acad. Sci. USA 89:6314-6318, 1992; Kreutzweiser et al., Ecotoxicol. Environ. Safety 28:14-24, 1994); heat shock inducible regulatory elements (Takahashi et al., Plant Physiol. 99:383-390, 1992; Yabe et al., Plant Cell Physiol. 35:1207-1219, 1994; Ueda et al., Mol. Gen. Genet. 250:533-539, 1996); and lac operon elements, which are used in combination with a constitutively expressed lac repressor to confer, for example, IPTG-inducible expression (Wilde et al., EMBO J. 11:1251-1259, 1992). An inducible regulatory element useful in the transgenic plants of the invention also can be, for example, a nitrate-inducible promoter derived from the spinach nitrite reductase gene (Back et al., Plant Mol. Biol. 17:9 (1991)) or a light-inducible promoter, such as that associated with the small subunit of RuBP carboxylase or the LHCP gene families (Feinbaum et al., Mol. Gen. Genet. 226:449 (1991); Lam and Chua, Science 248:471 (1990)).

Expression Using a Positive Feed Back Loop

In further embodiments, a plant can be engineered to overexpress AT10, AT7, AT15, or AT5 using a positive feedback loop to express AT10, AT7, AT15, or AT5 in a desired tissue. In such an embodiment, a promoter for use in an AT10, AT7, AT15, or AT5 expression construct is responsive to a transcription factor that mediates expression in the desired tissue. The AT10, AT7, AT15, or AT5 expression construct is used in a genentically modified plant comprising an expression construct encoding a transcription factor where expression is also driven by a promoter that is responsive to the transcription factor. Examples of such expression systems are provided in PCT/US2012/023182.

In some embodiments in which a positive feed back loop is employed, the plant is genetically modified to express a transcription factor that regulates the production of secondary cell wall. Examples of such transcription factors include NST1, NST2, NST3, SND2, SND3, MYB103, MBY85, MYB46, MYB83, MYB58, and MYB63 (See, e.g., Mitsuda et al., Plant Cell 17:2993-3006 (2005); Mitsuda et al., Plant Cell 19:270-80 (2007); Ohashi-Ito et al., Plant Cell 22:3461-73 (2010); Zhong et al., Plant Cell 20:2763-82 (2008); Zhong et al., Plant Cell 19:2776-92 (2007); Ko et al., Plant J. 60:649-65 (2009); and McCarthy et al., Plant Cell Physiol. 50:1950-64 (2009)).

Illustrative examples of gene and protein sequences and/or accession numbers for NST1, NST2, NST3, SND2, SND3, MYB103, MBY85, MYB46, MYB83, MYB58, and MYB63 are provided in PCT/US2012/023182.

In some embodiments, the polynucleotide encoding the transcription factor that regulates secondary cell wall production is operably linked to a promoter that is a downstream target of the transcription factor. Similarly, the AT10, AT7, AT15, or AT5 nucleic acid sequence is also linked to a promoter that is a downstream target of the transcription factor. The promoter may be the same promoter or different promoters. In such an embodiment, a promoter is suitable for use with the transcription factor that regulates secondary cell wall production if expression of the promoter is induced, directly or indirectly, by the transcription factor to be expressed, and if the promoter is expressed in the desired location, e.g., the stem of the plant.

In some embodiments, a native IRX1, IRX3, IRX5, IRX8, IRX9, IRX14, IRX7, or IRX10, GAUT13, or GAUT14 promoter, or active variant thereof, is employed.

Additional Embodiments for Expressing AT10, AT7, AT15, or AT5

In another embodiment, the AT10, AT7, AT15, or AT5 polynucleotide is expressed through a transposable element. This allows for constitutive, yet periodic and infrequent expression of the constitutively active polypeptide. The invention also provides for use of tissue-specific promoters derived from viruses including, e.g., the tobamovirus subgenomic promoter (Kumagai, Proc. Natl. Acad. Sci. USA 92:1679-1683, 1995); the rice tungro bacilliform virus (RTBV), which replicates only in phloem cells in infected rice plants, with its promoter which drives strong phloem-specific reporter gene expression; the cassava vein mosaic virus (CVMV) promoter, with highest activity in vascular elements, in leaf mesophyll cells, and in root tips (Verdaguer, Plant Mol. Biol. 31:1129-1139, 1996).

A vector comprising an AT10, AT7, AT15, or AT5 nucleic acid sequence will typically comprise a marker gene that confers a selectable phenotype on the cell to which it is introduced. Such markers are known. For example, the marker may encode antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, and the like.

AT10, AT7, AT15, or AT5 nucleic acid sequences of the invention are expressed recombinantly in plant cells as described. As appreciated by one of skill in the art, expression constructs can be designed taking into account such properties as codon usage frequencies of the plant in which the AT nucleic acid is to be expressed. Codon usage frequencies can be tabulated using known methods (see, e.g., Nakamura et al. Nucl. Acids Res. 28:292, 2000). Codon usage frequency tables are available in the art (e.g., from the Codon Usage Database at the internet site www.kazusa.or.jp/codon/.)

Additional sequence modifications may be made that are also known to enhance gene expression in a plant. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences that may be deleterious to gene expression. The G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence may also be modified to avoid predicted hairpin secondary mRNA structures.

Production of Transgenic Plants

As detailed herein, the present invention provides for transgenic plants comprising recombinant expression cassettes either for expressing heterologous AT10, AT7, AT15, or AT5 for overexpressing endogenous AT10, AT7, AT15, or AT5 using recombinant technology. It should be recognized that the term “transgenic plants” as used here encompasses the plant or plant cell in which the expression cassette is introduced as well as progeny of such plants or plant cells that contain the expression cassette, including the progeny that have the expression cassette stably integrated in a chromosome.

Once an expression cassette comprising a polynucleotide encoding an AT10, AT7, AT15, or AT5 polypeptide (or a polynucleotide sequence designed to suppress or inhibit expression of an AT gene, e.g., AT5, as described below) has been constructed, standard techniques may be used to introduce the polynucleotide into a plant in order to modify gene expression. See, e.g., protocols described in Ammirato et al. (1984) Handbook of Plant Cell Culture—Crop Species. Macmillan Publ. Co. Shimamoto et al. (1989) Nature 338:274-276; Fromm et al. (1990) Bio/Technology 8:833-839; and Vasil et al. (1990) Bio/Technology 8:429-434.

Transformation and regeneration of plants is known in the art, and the selection of the most appropriate transformation technique will be determined by the practitioner. Suitable methods may include, but are not limited to: electroporation of plant protoplasts; liposome-mediated transformation; polyethylene glycol (PEG) mediated transformation; transformation using viruses; micro-injection of plant cells; micro-projectile bombardment of plant cells; vacuum infiltration; and Agrobacterium tumeficiens mediated transformation. Transformation means introducing a nucleotide sequence in a plant in a manner to cause stable or transient expression of the sequence. Examples of these methods in various plants include: U.S. Pat. Nos. 5,571,706; 5,677,175; 5,510,471; 5,750,386; 5,597,945; 5,589,615; 5,750,871; 5,268,526; 5,780,708; 5,538,880; 5,773,269; 5,736,369 and 5,610,042.

Transformed plant cells derived by any of the above transformation techniques can be cultured to regenerate a whole plant that possesses the transformed genotype and thus the desired phenotype such as enhanced drought-resistance. Such regeneration techniques rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker which has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans et al., Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, pp. 124-176, MacMillilan Publishing Company, New York, 1983; and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, 1985. Regeneration can also be obtained from plant callus, explants, organs, or parts thereof. Such regeneration techniques are described generally, e.g., in Klee et al. Ann. Rev. of Plant Phys. 38:467-486, 1987.

One of skill will recognize that after the expression cassette is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed.

In some embodiments, the plant into which the expression construct comprising a nucleic acid sequence that encodes AT10, AT7, AT15, or AT5 (or that is designed to inhibit expression of AT5) is introduced is the same species of plant from which the AT sequence, and/or the promoter driving expression of the AT sequence, is obtained. In some embodiments, the plant into which the expression construct is introduced is a different species of plant compared to the species from which the AT and/or promoter sequence was obtained.

Plants that overexpress AT10, AT7, AT15, or AT5 can be identified using any known assay, including analysis of RNA, protein, or hydroxycinnamic ester content. With respect to this aspect of the invention, the plants have altered hydroxycinnamic acid levels, e.g., decreased ferulic acid. Hydroxycinnamic ester levels can be determined directly or indirectly. An example of an assay measuring hydroxycinnamic ester levels in the cell wall is provided in the Examples section. For this assay, biomass, or a cell wall extraction thereof, is treated with 2M NaOH. The resulting supernatant, or an extract thereof, can be analyzed for changes in hydroxycinnamate content via high performance liquid chromatography with UV absorbance detection or another similar method.

Modification of Plants to Decrease AT Expression

In one aspect, the invention also provides a plant in which expression of an AT gene as described herein, e.g., an AT5 gene is inhibited, thereby resulting in modified levels of hydroxycinnamic acid in the plant. As understood in the art, in some embodiments, it may be desirable to inhibit expression of AT10, AT7, or AT15 generally in a plant and restore expression in tissue of interests, e.g., grass cell wall. Techniques described in this section with reference to inhibition of AT5 can also be used to inhibit AT10, AT7, and/or AT15, if desired.

In some embodiments, the plant is modified to have a level of AT5 activity that is reduced throughout the entire plant. In some embodiments, the plant is modified to reduce AT5 activity in a subset of cells or tissues of the plant. The genetic background of the plant can be modified according to any method known in the art, such as antisense, siRNA, microRNA, dsRNA, sense suppression, mutagenesis, or use of a dominant negative inhibition strategy. In some embodiments, the level of expression of the protein is reduced.

Gene Silencing Techniques

In some embodiments, expression of a AT5 is inhibited by an antisense oligonucleotide. In antisense technology, a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the antisense strand of RNA will be transcribed. The expression cassette is then transformed into plants and the antisense strand of RNA is produced. In plant cells, it has been suggested that antisense RNA inhibits gene expression by preventing the accumulation of mRNA which encodes the enzyme of interest, see, e.g., Sheehy et al., Proc. Nat. Acad. Sci. USA, 85:8805-8809 (1988); Pnueli et al., The Plant Cell 6:175-186 (1994); and Hiatt et al., U.S. Pat. No. 4,801,340.

The antisense nucleic acid sequence transformed into plants will be substantially identical to at least a portion of the endogenous gene or genes to be repressed. The sequence, however, does not have to be perfectly identical to inhibit expression. Thus, an antisense or sense nucleic acid molecule encoding only a portion of an AT5-encoding sequence can be useful for producing a plant in which expression of AT5 is inhibited. For antisense suppression, the introduced sequence also need not be full length relative to either the primary transcription product or fully processed mRNA. Generally, higher homology can be used to compensate for the use of a shorter sequence. Furthermore, the introduced sequence need not have the same intron or exon pattern, and homology of non-coding segments may be equally effective. In some embodiments, a sequence of at least, e.g., 20, 25, 30, 50, 100, 200, or more continuous nucleotides (up to mRNA full length) substantially identical to a AT5 mRNA, or a complement thereof, can be used.

Catalytic RNA molecules or ribozymes can also be used to inhibit expression of a gene encoding an AT5 polypeptide. It is possible to design ribozymes that specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA. In carrying out this cleavage, the ribozyme is not itself altered, and is thus capable of recycling and cleaving other molecules, making it a true enzyme. The inclusion of ribozyme sequences within antisense RNAs confers RNA-cleaving activity upon them, thereby increasing the activity of the constructs.

A number of classes of ribozymes have been identified. One class of ribozymes is derived from a number of small circular RNAs that are capable of self-cleavage and replication in plants. The RNAs replicate either alone (viroid RNAs) or with a helper virus (satellite RNAs). Examples include RNAs from avocado sunblotch viroid and the satellite RNAs from tobacco ringspot virus, lucerne transient streak virus, velvet tobacco mottle virus, solanum nodiflorum mottle virus and subterranean clover mottle virus. The design and use of target RNA-specific ribozymes is described in Haseloff et al. Nature, 334:585-591 (1988).

Another method by which expression of a gene encoding an AT5 polypeptide can be inhibited is by sense suppression (also known as co-suppression). Introduction of expression cassettes in which a nucleic acid is configured in the sense orientation with respect to the promoter has been shown to be an effective means by which to block the transcription of target genes. For an example of the use of this method to modulate expression of endogenous genes, see Napoli et al., The Plant Cell 2:279-289 (1990); Flavell, Proc. Natl. Acad. Sci., USA 91:3490-3496 (1994); Kooter and Mol, Current Opin. Biol. 4:166-171 (1993); and U.S. Pat. Nos. 5,034,323, 5,231,020, and 5,283,184.

Generally, where inhibition of expression is desired, some transcription of the introduced sequence occurs. The effect may occur where the introduced sequence contains no coding sequence per se, but only intron or untranslated sequences homologous to sequences present in the primary transcript of the endogenous sequence. The introduced sequence generally will be substantially identical to the endogenous AT5 sequence intended to be repressed. This minimal identity will typically be greater than about 65%, but a higher identity can exert a more effective repression of expression of the endogenous sequences. In some embodiments, sequences with substantially greater identity are used, e.g., at least about 80%, at least about 95%, or 100% identity are used. As with antisense regulation, further discussed below, the effect can be designed and tested to apply to any other proteins within a similar family of genes exhibiting homology or substantial homology.

For sense suppression, the introduced sequence in the expression cassette, needing less than absolute identity, also need not be full length, relative to either the primary transcription product or fully processed mRNA. Furthermore, the introduced sequence need not have the same intron or exon pattern, and identity of non-coding segments will be equally effective. In some embodiments, a sequence of the size ranges noted above for antisense regulation is used, i.e., 30-40, or at least about 20, 50, 100, 200, 500 or more nucleotides.

Endogenous gene expression may also be suppressed by means of RNA interference (RNAi) (and indeed co-suppression can be considered a type of RNAi), which uses a double-stranded RNA having a sequence identical or similar to the sequence of the target gene.

RNAi is the phenomenon in which when a double-stranded RNA having a sequence identical or similar to that of the target gene is introduced into a cell, the expressions of both the inserted exogenous gene and target endogenous gene are suppressed. The double-stranded RNA may be formed from two separate complementary RNAs or may be a single RNA with internally complementary sequences that form a double-stranded RNA. Although complete details of the mechanism of RNAi are still unknown, it is considered that the introduced double-stranded RNA is initially cleaved into small fragments, which then serve as indexes of the target gene in some manner, thereby degrading the target gene. RNAi is known to be also effective in plants (see, e.g., Chuang, C. F. & Meyerowitz, E. M., Proc. Natl. Acad. Sci. USA 97: 4985 (2000); Waterhouse et al., Proc. Natl. Acad. Sci. USA 95:13959-13964 (1998); Tabara et al. Science 282:430-431 (1998); Matthew, Comp Funct Genom 5: 240-244 (2004); Lu, et al., Nucleic Acids Res. 32(21):e171 (2004)).

Thus, in some embodiments, inhibition of a gene encoding an AT5 polypeptide is accomplished using RNAi techniques. For example, to achieve suppression of the expression of a DNA encoding a protein using RNAi, a double-stranded RNA having the sequence of a DNA encoding the protein, or a substantially similar sequence thereof (including those engineered not to translate the protein) or fragment thereof, is introduced into a plant of interest. As used herein, RNAi and dsRNA both refer to gene-specific silencing that is induced by the introduction of a double-stranded RNA molecule, see e.g., U.S. Pat. Nos. 6,506,559 and 6,573,099, and includes reference to a molecule that has a region that is double-stranded, e.g., a short hairpin RNA molecule. The resulting plants may then be screened for a phenotype associated with the target protein, for example, screening for an increase in the extractability of sugar from the plants as compared to wild-type plants, and/or by monitoring steady-state RNA levels for transcripts encoding the protein. Although the genes used for RNAi need not be completely identical to the target gene, they may be at least 70%, 80%, 90%, 95% or more identical to the target gene sequence. See, e.g., U.S. Patent Publication No. 2004/0029283. The constructs encoding an RNA molecule with a stem-loop structure that is unrelated to the target gene and that is positioned distally to a sequence specific for the gene of interest may also be used to inhibit target gene expression. See, e.g., U.S. Patent Publication No. 2003/0221211.

The RNAi polynucleotides may encompass the full-length target RNA or may correspond to a fragment of the target RNA. In some cases, the fragment will have fewer than 100, 200, 300, 400, 500 600, 700, 800, 900 or 1,000 nucleotides corresponding to the target sequence. In addition, in some embodiments, these fragments are at least, e.g., 50, 100, 150, 200, or more nucleotides in length. In some cases, fragments for use in RNAi will be at least substantially similar to regions of a target protein that do not occur in other proteins in the organism or may be selected to have as little similarity to other organism transcripts as possible, e.g., selected by comparison to sequences in analyzing publicly-available sequence databases.

Expression vectors that continually express siRNA in transiently- and stably-transfected have been engineered to express small hairpin RNAs, which get processed in vivo into siRNAs molecules capable of carrying out gene-specific silencing (Brummelkamp et al., Science 296:550-553 (2002), and Paddison, et al., Genes & Dev. 16:948-958 (2002)). Post-transcriptional gene silencing by double-stranded RNA is discussed in further detail by Hammond et al. Nature Rev Gen 2: 110-119 (2001), Fire et al. Nature 391: 806-811 (1998) and Timmons and Fire Nature 395: 854 (1998).

Yet another way to suppress expression of an endogenous AT5 gene is by recombinant expression of a microRNA that suppresses a target (e.g., a gene encoding a lignin or xylan biosynthesis enzyme). Artificial microRNAs are single-stranded RNAs (e.g., between 18-25-mers, generally 21-mers), that are not normally found in plants and that are processed from endogenous miRNA precursors. Their sequences are designed according to the determinants of plant miRNA target selection, such that the artificial microRNA specifically silences its intended target gene(s) and are generally described in Schwab et al, The Plant Cell 18:1121-1133 (2006) as well as the internet-based methods of designing such microRNAs as described therein. See also, US Patent Publication No. 2008/0313773.

Another example of a method to reduce levels of AT5 employs riboswitch techniques (see, e.g., U.S. Patent Application Publication Nos. US20100286082, and US20110245326).

In some embodiments, the level of expression of AT5 is reduced by generating a plant that has a mutation in a gene encoding an AT5 enzyme. One method for abolishing or decreasing the expression of a gene encoding AT5 is by insertion mutagenesis using the T-DNA of Agrobacterium tumefaciens. After generating the insertion mutants, the mutants can be screened to identify those containing the insertion in the gene of interest. Mutants containing a single mutation event at the desired gene may be crossed to generate homozygous plants for the mutation (Koncz et al. (1992) Methods in Arabidopsis Research. World Scientific).

Alternatively, random mutagenesis approaches may be used to generate new alleles that will generate truncated or defective (non-functional or poorly active) enzymes or unstable RNA, or to disrupt or “knock-out” the expression of a gene encoding an AT5 enzyme using either chemical or insertional mutagenesis or irradiation.

Methods of Using Plants Having Modified AT10, AT15, AT7 and/or AT5 Expression

The nucleic acid constructs of the invention can be used to modulate the hydroxycinnamic acid of cell walls of essentially any plant, but in particular grass plants. The plant may be a monocotyledonous plant or a dicotyledonous plant. In some embodiments of the invention, the plant is a green field plant. In some embodiments, the plant is a gymnosperm or conifer. Thus, the invention has use over a broad range of plants, including species from the genera Asparagus, Atropa, Avena, Brassica, Cannabis, Citrus, Citrullus, Capsicum, Cucumis, Cucurbita, Daucus, Fragaria, Glycine, Gossypium, Helianthus, Heterocallis, Hordeum, Hyoscyamus, Lactuca, Linum, Lolium, Lycopersicon, Malus, Manihot, Majorana, Medicago, Nicotiana, Oryza, Panieum, Pannesetum, Persea, Pisum, Pyrus, Prunus, Raphanus, Secale, Senecio, Sinapis, Solanum, Sorghum, Trigonella, Triticum, Vitis, Vigna, and, Zea. In some embodiments, the plant is corn, switchgrass, sorghum, miscanthus, sugarcane, poplar, pine, wheat, rice, soy, cotton, barley, turf grass, tobacco, potato, bamboo, rape, sugar beet, sunflower, willow, and eucalyptus. In further embodiments, the plant is reed canarygrass (Phalaris arundinacea), Miscanthus×giganteus, Miscanthus sp., sericea lespedeza (Lespedeza cuneata), millet, ryegrass (Lolium multiflorum, Lolium sp.), timothy, Kochia (Kochia scoparia), forage soybeans, alfalfa, clover, sunn hemp, kenaf, bahiagrass, bermudagrass, dallisgrass, pangolagrass, big bluestem, indiangrass, fescue (Festuca sp.), Dactylis sp., Brachypodium distachyon, smooth bromegrass, orchardgrass, or Kentucky bluegrass among others. In some embodiments, the plant is an ornamental plant. In some embodiment, the plant is a vegetable- or fruit-producing plant. In some embodiments, the plant is a plant that is suitable for generating biomass, including plants as noted above, e.g., Arabidopsis, poplar, eucalyptus, rice, corn, switchgrass, sorghum, millet, miscanthus, sugarcane, pine, alfalfa, wheat, soy, barley, turfgrass, tobacco, hemp, bamboo, rape, sunflower, willow, Jatropha, and Brachypodium.

Plants, parts of plants, or plant biomass material from plants having modified AT10, AT15, AT7 and/or AT5 expression can be used for a variety of purposes. In embodiments, the plants, parts of plants, or plant biomass material may be used in a conversion reaction to generate an increased amount of bioenergy as compared to wild-type plants. For example, the plants, parts of plants, or plant biomass material can be used in a saccharification reaction to generate an increased amount of soluble and fermentable sugar compared to wild-type plants. In some embodiments, the plants, parts of plants, or plant biomass material are used to increase biomass yield or simplify downstream processing for wood industries (such as paper, pulping, and construction) as compared to wild-type plants. In some embodiments, the plants, parts of plants, or plant biomass material are used to increase the quality of wood for construction purposes. In some embodiments the plants, or parts of plants are used to improve the quality of textile fiber or simplify the downstream processing for textile industry. In some embodiments the plants, or parts of plants, are used as a raw material for pectin production.

Methods of conversion, for example biomass gasification, are known in the art. Briefly, in gasification plants or plant biomass material (e.g., leaves and stems) are ground into small particles and enter the gasifier along with a controlled amount of air or oxygen and steam. The heat and pressure of the reaction break apart the chemical bonds of the biomass, forming syngas, which is subsequently cleaned to remove impurities such as sulfur, mercury, particulates, and trace materials. Syngas can then be converted to products such as ethanol or other biofuels.

Methods of enzymatic saccharification are also known in the art. Briefly, plants or plant biomass material (e.g., leaves and stems) are optionally pre-treated with hot water, dilute acid, alkali, or ionic liquid followed by enzymatic saccharification using a mixture of cellulases and hemicellulases and pectinases in buffer and incubation of the plants or plant biomass material with the enzymatic mixture. Following incubation, the yield of the saccharification reaction can be readily determined by measuring the amount of reducing sugar released, using a standard method for sugar detection, e.g. the dinitrosalicylic acid method well known to those skilled in the art. Plants engineered in accordance with the invention provide a higher sugar yield as compared to wild-type plants.

In some embodiments, grass plants having modified AT10, AT15, AT7, or AT5 expression are used as forage plants for application in which an improvement in digestibility is desired.

EXAMPLES

The following examples are provided to illustrate, but not limit the claimed invention.

Example 1 The “Mitchell Clade” of BAHD Acyltransferases is Expanded and Diverged in Grasses

Mitchell et al. (2007) identified what is referred to in this examples section as the “Mitchell clade” of BAHD acyl CoA acyltransferases on the basis of high gene expression in grasses relative to dicots. We systematically characterized the distribution of this Glade in selected plant species and compared the Glade with other characterized BAHD proteins. We identified BAHD proteins from a diverse set of sequenced plants and analyzed the phylogenetic relationships among them and a reference set of BAHDs (Table I). To gain higher sensitivity relative to local sequence alignment (i.e., BLAST) for recognizing sequences with low, but potentially still significant, homology, we used a hidden Markov model to identify putative BAHD proteins (Finn et al., 2011). We then inferred an initial model of the phylogenetic relationships among the putative BAHD proteins from each genome and the set of biochemically characterized BAHD proteins cataloged by D'Auria (2006) with a neighbor joining algorithm (Tamura et al., 2011). Active BAHD proteins can be identified by a HXXXD motif. A variation of this motif can also be present in an active protein in which the histidine is replaced by a serine (see, e.g., one of the known biochemically active proteins for the family, BAPT (NCBI ID: AAL92459) involved in taxol biosynthesis (Walker et al., 2002).

As observed by Tuominen et al., the distribution of BAHD proteins varies among species (Table I, Supplemental FIG. 1, and LEB and PC, in prep). The “Mitchell clade” is embedded within Clade V, or Clade Va of Tuominen et al. The analysis revealed that the “Mitchell clade” includes a biochemically characterized banana alcohol CoA acyltransferase, BanAAT (Beekwilder et al., 2004), and is also related to a group of BAHD proteins that participate in taxol biosynthesis (FIGS. 1A-1B and Supplemental FIG. 1).

Using Bayesian analysis, we found that multiple proteins with similarity to the “Mitchell clade” are present in the grass genomes that were available at the time of the analysis, Sorghum bicolor and Brachypodium dystachion (Table I, Supplemental FIG. 1). In contrast, the annotated genomes of Arabidopsis thaliana, Glycine max, and Medicago truncatula encode only single members of this Glade. The other recently characterized cutin- and suberin-feruloyl transferases (Molina et al., 2009; Rautengarten et al., 2012), though part of Glade V, are not part of the “Mitchell clade”. The Glade is entirely absent from the annotated proteins of Populus trichocarpa and the primitive plants, Selaginella and Physcomietrella. Thus, the “Mitchell clade” appears to be conserved and expanded in grasses and banana relative to dicotyledonous species and more primitive plants. This is consistent with this Glade functioning in aspects of Commelinoid metabolism that diverge from metabolism of dicot and more basal plants, such as synthesis of type II cell walls.

The analysis described above also revealed that the “Mitchell clade” of BAHD acyltransferases was missing several members. Instead of possessing 12 members in rice (Mitchell et al., 2007; Piston et al., 2010), the group consists of 20 closely related members that are further subdivided into two subclades (i and ii, FIG. 1). In rice, the 10 genes in subclade i are all supported by Sanger-based expressed sequence tag (EST)-evidence; whereas, only 3 of the 10 members of subclade ii were identified via traditional EST sequencing (FIG. 1). In addition, the multi-species tree reveals that most proteins of subclade i are represented in all three grass species examined and are more similar to the non-grass proteins (Supplemental FIG. 1). In contrast, subclade ii contains more species-specific expansions and/or contractions, consistent with the possibility that some of the members are pseudogenes. To facilitate communication about the putative “Mitchell clade” acyltransferases, we have given the Glade members of rice preliminary names with the format Oryza sativa acyltransferase, OsAT1 through OsAT20. As mentioned above, OsAT4 was recently named PMT and found to be capable of esterifying monolignols (Withers et al., 2012).

Screen of Mutants for Altered Cell Wall Hydroxycinnamic Acid Content

We screened indexed rice mutants related to Mitchell clade” of BAHD CoA acyltransferases for altered cell wall content. Table II describes the mutant lines that we characterized. We screened progeny of each of these lines for the presence of the insertion, did not detect an insert in four lines, and for two lines, did not identify any progeny that were homozygous for the insert (Table II).

For the remaining 11 lines, we characterized the alkali-labile hydroxycinnamoyl ester content of cell wall alcohol insoluble residue (AIR) from leaves and leaf sheaths. We compared side tillers of homozygous, mutant and negative segregant, wild-type plants seven to ten weeks after planting. From this, we found four possible cell wall hydroxycinnamic acid phenotypes (Table II, FIG. 2). Three of the preliminary phenotypes were in putative mutants of subclade i proteins, and one was a mutant in a subclade ii protein. Homozygous mutant progeny of 2A-20021, predicted to increase expression of OsAt5, exhibited reduced p-CA in leaf sheaths relative to negative segregant wild-type progeny (˜50% less). Homozygous mutant progeny of 2A-40095, possessing the transcriptional activator sequences but inserted toward the end of the coding sequence for OsAt7, exhibited reduced FA in leaf sheaths (˜60% less). Homozygous mutant progeny of 4A-03423 (OsAT10-D1), however, which were predicted to increase expression of OsAt10, exhibited reduced FA (˜60% less) and increased p-CA (˜300% more) in sheaths and leaves. Homozygous mutant progeny of 1B-00523, which were predicted to increase expression of OsAT15, a subclade ii member, exhibited reduced FA in leaves relative to negative segregant, wild-type progeny (˜60% less). In contrast, the other lines showed no change in FA or p-CA in the developmental stages and tissues examined. For example, our experiment included line 5A-00394, which is predicted to have activated expression of a putative rice exostosin (GT47) gene, LOC_Os10g10080. This line showed no alteration in cell wall hydroxycinnamic acids in leaf blades or sheaths (FIG. 2).

Gene Expression and Developmental Phenotypes of OsAT10-D1

The T-DNA insertion site for line 4A-03423, hereafter referred to as OsAT10-D1, is approximately 8.5 kb downstream of the transcriptional start site for OsAt10 (FIG. 3A). The insert is oriented so that the activating sequences are proximate to OsAt10 and thus is in range observed to activate expression (Jeong et al., 2006). RT-qPCR indicated that the expression of OsAt10 was indeed increased by >100-fold in the leaves of homozygous OsAT10-D1 plants (FIG. 3B). In OsAT10-D1, the expression genes other than OsAt10 that were proximate to the site of the T-DNA insertion did not vary significantly relative to the wild type (FIG. 3B). The expression of related OsAt genes did not vary significantly in OsAT10-D1 (Supplemental FIG. 2), reducing the possibility that the observed phenotype is due to compensation at the level of gene expression of a related acyltransferase. OsAT10-D1 lines exhibited no change in size and dry mass at maturity (FIGS. 4A-4B). However, a ˜20 to 30% decrease in total seed mass per plant for the mutant compared to the wild type (FIG. 4C) was observed.

Cell Walls of OsAt10 Over Expression Lines are Heritable Altered in Ester-Linked Hydroxycinnamic Acids

For OsAT10-D1, we confirmed the inheritance of the altered cell wall hydroxycinnamate phenotype in young leaves and mature tillers of plants from two subsequent generations (FIGS. 5A-5D and Supplemental FIG. 3). This line has a ˜50% decrease in ester-linked FA in young leaf tissue (FIG. 5A). The same tissue shows an ˜300% increase in ester-linked p-CA (FIG. 5B). The change in both components is most clearly exhibited as a change in the ratio of FA to p-CA (FIG. 5C). The ratio is the most reliable as it is independent of potential variation in the absolute amounts due to variation in sample mass and extraction efficiency. We were also able to quantify the four most abundant ferulate dimers. ough signals were low for some dimer species, most showed decreases compared to wild-type amounts (FIG. 5D). We found that the dimers decreased proportionally to the decrease in FA in the young leaf tissues (FIG. 5D). This can be most clearly seen as the similar ratio of FA compared to the sum of the dimer species (FIG. 5D). In addition, we found similar trends but less extreme changes in pools of total aerial tissues harvested after senescence for the same plants from each genotype (FIGS. 5A-5D). These mature straw samples possessed a ˜40% less FA and −80% more p-CA. Measurements were independent of whether total, AIR or destarched AIR preps were used, but these different samples do show the technical replicate-ability of the analysis.

To gather further evidence that the phenotype in the activation tagged line was due to over expression of OsAT10, we generated two additional OsAt10 over expression lines utilizing the maize ubiquitin) promoter (FIGS. 6A-6C). Contrary to our typical experience for high efficiency transformation with the japonica cultivar, Kitaake (Jung et al., 2008), we were only able to regenerate two independent transformants that possessed the transgene from tissue culture (FIG. 6A). This result suggest that the OsAt10 construct interferes with transformation efficiency. Both of the confirmed transgenic lines did show increased expression of OsAt10 compared to the non-transgenic plants (FIG. 6A). Furthermore, AIR from young leaf tissue of the primary transgenics also exhibited a qualitatively similar change in hydroxycinnamic acids compared with the OsAT10-D1 line (FIG. 6B). In particular, the ratio of FA:p-CA was dramatically decreased in both lines, though the absolute amounts of FA and p-CA varied relative to the non-transgenics. Specifically, Ubi::OsAt10-4 has a sharp decrease in FA, with a relatively smaller increase in p-CA and Ubi::OsAt10-5 showed no change in FA, but a dramatic increase in p-CA (FIG. 6B). As with the other over expression lines, the FA:diferulate ratios do not vary from those observed for the non-transgenics (FIG. 6C).

The Difference in OsAT10-D1 Hydroxycinnamates is Predominantly TFA-Soluble and is Linked to a 5-Carbon Sugar

In grasses, hydroxycinnamoyl esters have been found to be attached to matrix polysaccharides, glucuranoarabinoxylan or xyloglucan, or to lignin. We examined which cell wall fraction harbored the alteration in FA and p-CA in the OsAT10-D1 mutant. To accomplish this, we subjected AIR from mutant and wild-type mature rice straw with a relatively mild, 50 mM trifluoroacetate (TFA) treatment to release the matrix polysaccharides. At multiple time points, we removed a fraction of the supernatant. We then saponified both the supernatants and pellet with the typical 2 N NaOH treatment followed by HPLC analysis of the products. The results demonstrated that the alteration in FA and p-CA amounts in OsAT10-D1 is primarily in the matrix polysaccharide fraction of the cell wall (FIGS. 7A-7C). For both the wild type and OsAT10-D1, the FA is predominantly associated with the TFA fraction, with less than 20% of the FA remaining in the pellet after TFA treatment for both genotypes (FIG. 7A). The reverse is observed for the p-CA for the wild type, in which ˜70% of the p-CA remains in the pellet (FIG. 7B). However, for the mutant only 55% of the p-CA is in the pellet after TFA treatment, though the absolute amount of p-CA in the TFA pellet are very similar for the wild type and mutant (FIG. 7B). Thus, we conclude the additional p-CA in the cell wall of the OsAT10-D1 is in the TFA-soluble matrix polysaccharide fraction. This can be clearly seen in the FA:p-CA ratio plot, in which the ratio of FA:p-CA is most drastically changed in the supernatants after TFA treatment; whereas, the FA:p-CA ratio is the same within error for the mutant and wild type in the residue remaining after TFA treatment (i.e., pellet, FIG. 7C). These data suggest that in mature rice straw, the change in p-CA in the matrix polysaccharide fraction approaches a ˜300% increase of OsAT10-D1 over the wild type, rather than the smaller ˜70% increase when total ester-linked p-CA is considered. Consistent with the typical location of p-CA on lignin, this magnitude of increase in the mutant compared to the wild type is more similar to that seen in young leaf tissue, which in the wild type possess a relatively lower percentage of p-CA compared to FA (FIGS. 5A-5D).

Further analysis of the TFA soluble fractions supports the assertion that the glucuranoarabinoxylan is modified by OsAt10 activation. First, the sugars released by TFA treatment in this experiment predominantly consist of xylose, consistent with the model that OsAT10 functions in arabinoxylan modification (Supplemental FIG. 4). In contrast, the pellet contains less than 20% of the total amount of xylose. Furthermore, via LC-MS, we detected two major new ion peaks in the TFA-solubilized ethylacetate extract compared to extract that had been treated with NaOH or with hydroxycinnamate standards (FIG. 8A). The mass spectra of these peaks are consistent with the major unknown peak in the mutant (unknown peak 1) consisting of p-CA esterified to a five-carbon sugar (m/z=295.0285, FIG. 8B); whereas, the predominant peak in the wild type (unknown peak two) is consists of FA esterified to a five carbon sugar (m/z=325.083, FIG. 8C). Because arabinose and xylose have the same molecular weight they are indistinguishable in this experiment; however, our strong expectation from nuclear magnetic resonance (NMR) data from the literature is that the esterified sugar is arabinose (Buanafina, 2009; Ralph, 2010). Relative quantification of the ion counts of each of these peaks in the mutant vs. the wild type is consistent with the results measured via HPLC. That is, compared with the wild type, OsAT10-D1 has ˜4.6-fold more pCA-sugar and 2.5-fold less FA-sugar (FIG. 8A). The relative amounts of FA and p-CA after saponification are also consistent with our previous results (FIG. 8A).

The OsAT10-D1 Line has an Increase in Cell Wall Glucose Content

Compensatory changes are often seen among the components of the cell wall (Humphrey et al., 2007). Quantification of sugars released by acid treatment of total, AIR, and destarched (ds) AIR preparations suggests that the glucose content is increased by ˜20% (weight/weight) in AIR and dsAIR for the mutant relative to the wild type (FIG. 9A). We observed the difference both with TFA treatment, which liberates matrix polysaccharides and amorphous cellulose, and when the TFA residue is further treated with sulfuric acid, which liberates cellulose (FIG. 9A). That the difference persists after destarching is consistent with a change in the cell wall content, not starch. By mass, we did not observe any other significant changes in sugar amounts in the mutant compared to the wild type (Supplemental FIG. 5). Expressing sugar data as percent of molecules (mol %) is more precise because it excludes weighing and other experimental errors. When the TFA-solubilized sugars are expressed in terms of mol %, the data also indicate an increase in glucose content, on the order of 10 to 20% (FIG. 9B). Xylose, arabinose, and the sum of minor cell wall sugars decrease proportionally to the glucose increase (10-20%), suggesting that the change in cell wall polysaccharide content in the mutant is isolated to the glucose-containing polymers.

The OsAT10-D1 Shows No Alterations in Lignin Content or Composition

To further explore the extent of cell wall changes in the mutants relative to the wild type, we also measured lignin content and composition. We hypothesized that the possible alteration in pools of hydroxycinnamyl-CoA adducts in the OsAT10-D1 line might lead to alterations in lignin amount or content, in terms of syringyl (S), guiacyl (G), and coumaryl (H) subunits. Due to the presence of H residues in grass lignin, all methods of lignin analysis are not equally accurate for grasses relative to dicots. For our analysis, we used two methods suitable for grasses—acetylbromide solubilization (Grabber et al., 1996; Fukushima and Hatfield, 2004) and pyrolysis-molecular beam mass spectrometry (py-MBMS) (Evans and Milne, 1987; Agblevor et al., 1994). “Lignin” analyses of whole tissue or AIR typically include all classes of phenylpropanoids, both esterified and non-esterified, though some esterified hydroxycinnamates are associated soley with arabinoxylan. Since our previous analysis had determined that there is a difference in OsAT10-D1 in ester-linked phenolics, we quantified lignin content and composition with and without removing esterified hydroxycinnimates via saponification.

OsAT10-D1 mature aerial tissue, and separate, young leaf and sheath samples show no significant difference in mass percent acetylbromide soluble lignin after saponification relative to the wild type. We obtained a similar result via py-MBMS, which also revealed no difference in the S:G lignin ratio in the mutant compared to the wild type after saponification. For OsAT10-D1, we also collected py-MBMS data for unprocessed straw and AIR. When analyzed together via principle component analysis (PCA), the first component clearly separates the saponified and unsaponified samples and explains 85% of the variation between the samples (not shown). Separate analysis of the saponified and unsaponified samples reveals distinctions between the wild type and mutant in the unsaponified samples (FIG. 10A). Principle component 1 (PC1) explains the alcohol extraction (30% of the variation) and principle component 2 (PC2) explains differences between the wild-type and mutant samples (19% of the variation). The loadings for PC2 show that the major ions that distinguish the wild-type and mutant samples are phenolics (FIG. 10B). Thus, the MS fragmentation pattern is consistent with an interpretation in which there is an increase of p-CA, as reflected by peaks 120, 94, and 91, and a decrease in ferulic acid, as reflected in the drop in the coniferyl ion, peak 150 (Evans and Milne, 1987). Note that the “tails” of phenylpropanoid molecules are typically absent in these spectra due to MS fragmentation. The observed differences in phenylpropanoids between OsAT10-D1 and the wild type are likely associated with ester-linked hydroxycinnamates and not lignin, because PCA no longer distinguishes the samples after saponification (FIG. 10C).

A limitation of the pyrolysis method for determining lignin composition is that it inaccurately measures H-lignin, which volatilizes poorly and instead turns to char upon heating. Because of the increase in p-CA, a precursor of H-lignin, in OsAT10-D1 cell walls relative to the wild type, we sought to determine whether there is an increase in the char content of OsAT10-D1 using a thermogravimetric (TG) pyrolysis instrument. Duplicate runs per genotype of the TG did not detect a difference in the mass remaining from mature straw after pyrolysis (Supplemental FIG. 7), again consistent with there being no difference in core lignin composition or content between OsAT10-D1 and the wild type.

The OsAT10-D1 Line Shows an Increase in Saccharification

Several researchers have observed a correlation between ferulate esters in grass biomass and digestibility among diverse canarygrass and lolium accessions (Lam et al., 2003; Casler and Jung, 2006). The phenotype of the OsAt10-D1 line provided the opportunity to determine whether there is also an increase in enzymatic digestibility with reduced FA content when comparing two near-isogenic plant lines, with little to no variation besides the difference in cell wall hydroxycinnamic acid content. We found that destarched AIR after mild pre-treatment followed by incubation with a cellulase cocktail and β-glucosidase resulted in the release of approximately 20% more reducing sugar from the mutant compared with the wild type at all time points examined (FIG. 11A). We note that this might be explained solely by the increase in glucose content, which is quantitatively similarity.

We also determinee if the improvement in digestibility impacted a biological saccharification agent. For this, we exposed acid-explosion pretreated, coarsely chopped rice straw from the wild type and OsAT10-D1 to the mesophilic fungus, Penicillium sp. YT02. This recently characterized fungus shows significantly higher xylanase and β-glucosidase with various insoluble lignocellulosic substrates in comparison with the commonly used fungal strain, Trichoderma reesei (ATCC 24449) (Kovacs et al., 2009), and may be a promising strain for industrial bioprocessing of cellulosic plant biomass (L. Gao and J. Zhou, in prep). Qualitatively consistent with the enzymatic deconstruction results, YT02 incubation released more glucose, xylose, and arabinose into the medium from acid explosion pretreated OsAT10-D1 straw than from wild-type straw (FIG. 11B). Averaged over the entire time course (12 to 120 hours), the improvement in yield is more dramatic with the fungus than with enzymes alone, with the fungus releasing 46% more glucose, 82% more xylose, and 25% more arabinose for a total sugar yield increase of ˜40%. In the fungal treatments, the biomass-derived sugars initially accumulate, due to the action of enzymes excreted by the fungus. At later time points (>72 hrs.), the fungus metabolizes the sugars, incorporating them into fungal biomass. Cellulase and β-glucosidase enzymatic activity in the slurry is unchanged on the mutant straw (FIG. 11C and Supplemental FIG. 8), suggesting that the fungus grew similarly on both. In contrast and of relevance to the nature of the change caused by the increased expression of OsAT10, xylanase activity is dramatically enhanced, especially at later time points (FIG. 11C).

OsAT5

FIGS. 19A-19B provide the genomic positions and gene expression data of the OsAT5-D1 activation tagged line. Genomic positions and gene expression data for the OsAT5-D1 activation tagged line (FIG. 19A) Representation of the portion of the rice chromosome near the T-DNA insertion site. Exons are represented by wide bars with the direction of transcription indicated by arrows. The insertion site is represented by the triangle, with the left border, nearest the transcriptional enhancer elements, represented by ‘L’. cDNA Regions targeted for amplification in qPCR are depicted as black bands. RT stands for retrotransposon and hypoth indicates hypothetical. (FIG. 19B) Average normalized gene expression determined via qPCR shows that among genes within 20 kbp of the insertion site only acyltransferase expression is altered significantly in young leaves of homozygous plants with the T-DNA insertion (hashed) compared with negative segregants (solid). Error bars represent the standard deviation of 3-4 biological replicates. Genes with significantly higher expression (p<0.01, Student's t-test) are marked with an asterisk.

FIGS. 20A-20D provides data demonstrating that OsAT5-D1 shows alterations in cell wall hydroxycinnamic acids. Data are for two separately grown batches (#1 and #2) of plants of a near isogenic family lacking the insert (grey bars, progeny of the near isogenic wild type line 2A-20021.10.2) and a family homozygous for the insert (cross-hatched bars, progeny of the OsAT5-D1 mutant line 2A-20021.11.7). Samples for batch #1 were harvested from seedlings 35 days post germination. The expanding leaf samples for batch #2 were harvested at 8 weeks post germination and the mature tiller at 16 weeks post germination. Values are the average of 5 to 12 individual plants. Error bars mark the 95% confidence interval for the mean. * indicates significance via Student's t-test at p<0.05 and ** indicates significance at p<0.01. (FIG. 20A) Ferulic acid content in an alcohol insoluble residue (AIR) preparation. (FIG. 20B) p-Coumaric acid content from AIR. (FIG. 20C) The ratio of ferulic acid (FA) to p-coumaric acid (CA), which is not subject to weighing or extraction efficiency errors. (FIG. 20D) Major FA dimer species and the ratio of FA to dimer for the Batch #1 expanded leaf samples.

FIGS. 19A-19B. Genomic positions and gene expression data of the OsAT5-D1 activation tagged line. Genomic positions and gene expression data for the OsAT5-D1 activation tagged line (FIG. 19A) Representation of the portion of the rice chromosome near the T-DNA insertion site. Exons are represented by wide bars with the direction of transcription indicated by arrows. The insertion site is represented by the triangle, with the left border, nearest the transcriptional enhancer elements, represented by ‘L’. cDNA Regions targeted for amplification in qPCR are depicted as black bands. RT stands for retrotransposon and hypoth indicates hypothetical. (FIG. 19B) Average normalized gene expression determined via qPCR shows that among genes within 20 kbp of the insertion site only acyltransferase expression is altered significantly in young leaves of homozygous plants with the T-DNA insertion (hashed) compared with negative segregants (solid). Error bars represent the standard deviation of 3-4 biological replicates. Genes with significantly higher expression (p<0.01, Student's t-test) are marked with an asterisk.

FIGS. 20A-20D. OsAT5-D1 shows alterations in cell wall hydroxycinnamic acids. Data are for two separately grown batches (#1 and #2) of plants of a near isogenic family lacking the insert (grey bars, progeny of the near isogenic wild type line 2A-20021.10.2) and a family homozygous for the insert (cross-hatched bars, progeny of the OsAT5-D1 mutant line 2A-20021.11.7). Samples for batch #1 were harvested from seedlings 35 days post germination. The expanding leaf samples for batch #2 were harvested at 8 weeks post germination and the mature tiller at 16 weeks post germination. Values are the average of 5 to 12 individual plants. Error bars mark the 95% confidence interval for the mean. * indicates significance via Student's t-test at p<0.05 and ** indicates significance at p<0.01. (FIG. 20A) Ferulic acid content in an alcohol insoluble residue (AIR) preparation. (FIG. 20B) p-Coumaric acid content from AIR. (FIG. 20C) The ratio of ferulic acid (FA) to p-coumaric acid (CA), which is not subject to weighing or extraction efficiency errors. (FIG. 20D) Major FA dimer species and the ratio of FA to dimer for the Batch #1 expanded leaf samples.

Discussion

Hydroxycinnamyl esters in cell walls influence basic and applied plant traits including growth properties, disease resistance, and food and feed quality (Santiago et al., 2007; Buanafina, 2009). The molecular mechanism of incorporation of hydroxycinnamates into cell walls remains largely obscure. Here, we present results showing that over expression of OsAt10 in the OsAT10-D1 line decreases FA and increases p-CA in leaf blades, leaf sheaths, and mature straw (FIG. 5). We have also confirmed that over expression of OsAt10 in two other independent lines, Ubi::OsAt10-4 and Ubi::OsAt10-5, alters the ratio of FA to p-CA in a manner similar to OsAT10-D1, namely by causing a dramatic decrease in the FA:p-CA ratio relative to wild-type genotypes (FIGS. 6A-6C).

Distribution of BAHD CoA Acyltransferases Across Plants

Our phylogenetic analysis shows that, with one exception, sequenced angiosperms that we examined have annotated proteins within the “Mitchell clade” of BAHD acyl CoA-utilizing acyltransferase proteins, identified by being highly expressed in grasses (Mitchell et al., 2007). However, there has been a distinct expansion of this Glade in grasses, with 12-20 members in grasses compared to 0-2 in other species (Table I). The presence and expression of a protein in the Mitchell clade in banana (order Zingerberales, BanAAT (Beekwilder et al., 2004)), is consistent with the presence of hydroxycinnamates in banana cell walls (Carpita, 1996).

A mutant in the most closely related Arabidopsis protein, AT3G62160, was recently examined for a change in hydroxycinnamates in the cell wall and other extracellular polymers, though no differences were identified (Rautengarten et al., 2012). Though the function of the Arabidopsis protein remains to be determined, that result is consistent with a model of neofunctionalization or subneofunctionalization of the “Mitchell clade” of BAHD acyltransferases in Commelinoid monocots (He and Zhang, 2005). In this model, a duplicated “Mitchell clade” member in the progenitor of Commelinoids acquired the ability to modify a cell wall-related substrate. Subsequently, the conservation of additional Glade members that we observe is consistent with selection for further additional gene duplication events.

The Cell Wall Target of OsAT10 is Arabinoxylan

Previous results have found that p-coumaroyl esters are almost exclusively bonded to lignin; whereas, FA is predominantly esterified to glucuranoarabinoxylan. However, enzymatic release experiments have provided some prior evidence that p-CA is also incorporated into the polysaccharides of grass cell walls (Mueller-Harvey et al., 1986; Ishii et al., 1990; Faulds et al., 2004). We find that mature rice straw has ˜20% of p-CA associated with matrix polysaccharide (FIGS. 7A-7C). This may also be the location of the p-CA in the young leaf tissue, which we expect to have very low lignin amounts (FIGS. 6A-6C). We found that the hydroxycinnamic acid changes in OsAT10-D1 are predominantly on the TFA-soluble matrix polysaccharide fraction, not the acid-resistant lignin (FIGS. 7A-7C). Indeed, we were able to confirm that the hydroxycinnamoyl groups in the TFA-released fraction are ester-linked to a 5-carbon sugar. Since this sugar-hydroxycinnamoyl species migrate in narrow bands in the LC-MS analysis, we strongly suspect that these represent only arabinose esters, which have been commonly described (Mueller-Harvey et al., 1986; Buanafina, 2009). Thus, it is unlikely that this peak also consists of feruloylated-xylose, which has been described from bamboo xyloglucan (Ishii et al., 1990). Furthermore, we have no evidence to suggest that OsAT10 functions as a p-coumaroyl CoA monolignol acyltransferase that has been described in recent publications (Hatfield et al., 2009; Withers et al., 2012). Rather, it seems likely that the native function of OsAT10 is to incorporate p-CA into cell wall 5-carbon sugars, likely the arabinose of arabinoxylan. This is consistent with the notion that different “Mitchell clade” members may have different functions.

We observed that OsAT10-D1 had an ˜300-fold increase in gene expression, but only a 3-fold increase in p-CA. While this could be caused by the cell wall phenotype being an indirect result of increased OsAt10 expression, this trivial explanation is unlikely based on previous results. The observations that silencing “Mitchell clade” members decreases rice cell wall hydroxycinnamate content (Piston et al., 2010) and that biochemical analysis of one of them, PMT (OsAT4), demonstrates function on a cell wall substrate makes the trivial explanation unlikely. Instead, the difference suggests that other parts of the cell wall hemicellulose-incorporation pathway are limiting in the presence of the excess amount of acyltransferase. Indeed, dramatic changes in, for example, the monolignol biosynthesis enzymes, 4-coumaryl CoA ligase of Arabidopsis, cause comparatively small changes in enzyme activity and lignin composition (Lee et al., 1997). Assuming that the altered polysaccharide is arabinoxylan, one possibility is that the frequency of hydroxycinnamoyl-arabinose incorporation is controlled by the glycosyltransferases that synthesize arabinoxylan. Another observation that remains to be completely resolved is the decrease in sugar-feruloylation that accompanies the increase in p-coumarylation in cell walls of mutant plants. Some specificity in the level of modification of arabinose may explain this observation. Alternatively or in addition, since p-CA is a precursor of FA, the increased activity of the putative p-CA transferase, OsAT10, may reduce the amount of feruloyl-CoA available for modification of the hemicellulose. Further experiments will be needed to test these models.

“Mitchell Clade” Acyltransferase Have Different Effects on Cell Wall Hydroxycinnamoyl Esters

Both our data and that of Piston et al. (2010) provide genetic evidence that changing the expression of “Mitchell clade” CoA acyltransferases alters the amounts of cell wall hydroxycinnamyl esters. Superficially, our result that OsAT10 over expression decreases cell wall ferulate appears to conflict with that of Piston et al. (2010), who reported that simultaneous reduced expression of OsAT6 through OsAT10 (i.e., construct pAFT-B) causes a ˜20% reduction in the amount of FA in mature leaves. One possibility is that in OsAT10-D1 a change in expression of other related acyltransferases causes the observed phenotype. However, our results showing that there is no measurable change in selected related acyltransferases in the over expression lines (Supp FIG. 2), make this model less likely.

Instead, the various results with “Mitchell clade” members is consistent with the model that differing OsATs have different functions. First, this model explains the apparent conflict between Piston et al.'s results and ours. If all of the OsATs function to incorporate FA into arabinoxylan, it seems likely that the effect of reducing expression 2- to 5-fold for four to five OsAT members would give greater than the observed 20% reduction in FA. Further, Piston et al. detected no effect on wall hydroxycinnamates in lines with simultaneously reduced expression of OsAt1, OsAt2, OsAt11, and OsAt12 (i.e., construct pAFT-A). Thus, we suspect that Piston et al. observed small or no effects because their constructs caused multiple small effects. Indeed, while several studies have found that BAHD acyltransferases often have promiscuous specificities (D'Auria, 2006), work with anthocyanidin-malonyl transferases (Dm3MAT1), have measured discrimination for a hydroxylated substrate over a maloynalted one (Unno et al., 2007). Thus, it is not improbable to hypothesize that different acyltransferases may have differential affinities for the two hydroxycinnamyl CoA adducts. This is also consistent with the report of Withers et al. that OsAT4 (PMT) acts on monolignols (Withers et al., 2012), rather than polysaccharides.

Glucose Polysaccharide, but not Lignin, Compensation in OsAT10-D1

Several cases of compensatory changes in plant cell wall composition have been observed. For example, the cell walls of an Arabidopsis mutant with dramatically reduced xylan, irx10irx10L, possess by mass more glucose, arabinose, and galactose compared with those of wild-type plants (Wu et al., 2009). Also, other Arabidopsis and rice xylan mutants have reduced lignin content (Scheller irx 9 and irx 7 paper, (Chen et al., in prep)). Similarly, poplar saplings (Populus tremuloides) in which a phenylpropanoid biosynthesis gene for 4-coumaryl-CoA ligase is silenced produce less lignin but more cellulose (Hu et al., 1999). However, compensatory changes are not uniformly observed in response to reduced amounts of a particular cell wall component. For example, no consistent changes in polysaccharide content are observed in switchgrass plants with lignin reduced by silencing of the phenylpropanoid biosynthesis genes that encode caffeic acid 3-O-methyltransferase or cinnamyl alcohol dehydrogenase (Fu et al., 2011; Fu et al., 2011).

The mature cell walls of OsAT10-D1 exhibits a ˜15 to 20% increase by mass and mol % in both TFA-soluble glucose, corresponding to mixed linkage glucose and amorphous cellulose, and TFA-insoluble glucose, representing crystalline cellulose (F). The increase in crystalline cellulose is of a similar magnitude to that observed in poplar silenced for 4-coumaryl-CoA ligase (15%, (Hu et al., 1999)). In contrast, chemical, mass spectrometry, and thermogravimetric assays did not detect alterations in lignin content or composition in the OsAT10-D1 mutant line (Table III, FIGS. 9A-9B, and Supplemental FIG. 5). This suggests that lignin amounts are not sensitive to changes in phenylpropanoid pathway flux that may be caused by increased OsAT10 activity. The observations that FA and glucose levels change but lignin does not might be due to spatial and temporal separation of the incorporation of hydroxycinnamates into a precursor of arabinoxylan and the synthesis of lignin. Generally, our results contribute to an emerging view that plants possess specific molecules that are able to sense and trigger responses to specific changes in cell wall composition and/or function; however, the nature of those sensors remains obscure (Humphrey et al., 2007).

Cell Wall Hydroxycinnamyl Esters May Contribute to Plant Reproduction

Correlative studies suggest that FA dimerization has a role in halting plant growth via inhibition of cell wall elongation and expansion (MacAdam and Grabber, 2002; Obel et al., 2002; Sasayama et al., 2011). Thus, we might have expected plants with reduced FA dimer content to either be smaller, due to decreased ability to support themselves, or be larger, due to greater expansion of cells during growth. Indeed, the progeny of a maize line with reduced ferulate esters at the seedling stage, has recently been found to increase biomass by ˜8% in field trials (Jung and Phillips, 2010). However, we observed no effect on vegetative growth for greenhouse-grown OsAt10 over expression lines (FIG. 4). We were also unable to detect changes in the breaking force of OsAT10-D1 seedling leaves compared with those of the negative segregant (FL, R. Gan, and LEB unpublished), suggesting that this modification does not cause changes in leaf biophysics. OsAT10-D1 does exhibit reduced seed yields per plant by ˜20% (FIG. 4). This observation correlates with the difficulty of isolating homozygous knockout lines for various OsATs (Table II, F. Piston and J. Dubcovsky personal communication). On the other hand the low ferulate maize lines did not exhibit a change in ear mass at the stage examined (Jung and Phillips, 2010). From a practical perspective, restoring grain yield in plants engineered to over express OsAt10 would be an important consideration for development of a dual-use crop for both food and biofuel/feed purposes, but would be less crucial for dedicated fuel and feed grasses. One way to accomplish this might be to use a promoter with low expression in reproductive tissues.

Heightened Saccharification of OsAT10-D1

A major impetus for this work was to understand if a specific genetic reduction of the amount of cell wall-associated FA would improve the yields of cell wall sugars from modified plants for biofuel and feed production. We found that the decreased amount of FA and proportional decrease in FA dimers releasable from OsAT10-D1, did indeed lead to greater sugar yields in both enzymatic and fungal saccharification assays (FIGS. 11A-11C). However, the quantitative similarity between the improvement in cellulose-mediated digestion and cell wall glucose content (˜20%) suggest that with the mild pretreatment conditions used the improvement in enzymatic digestibility may not be due to altered cellulose accessibility, but rather cellulose content. On the other hand, the larger improvement in glucose yield (˜45%) from acid pretreatment and fungal digestion is consistent with improvements in the accessibility of glucose-containing polysaccharides. The improvement in fungal xylose release was particularly dramatic (85%) and correlates with an increase in fungal xylanase production (FIGS. 11A-11C), as if due to a positive feedback loop between xylose and xylanase expression. The enhanced xylanase activity of YT02 on the mutant straw is consistent with the model that the modifications in the mutants are on the xylan polymer, which is made more accessible by reduced ability to cross-link with each other and lignin. The acid-based pretreatment and the synthesis by the fungus of a suite of enzymes, presumably including diverse xylanases, in the fungal assay might have accentuated the effects of the reduced ferulate content of the mutant relative to the wild type. In contrast, we do not expect that there is a major improvement in the quality of the xylan of the OsAT10-D1 because the xylan in the mutant appears to have higher absolute hydroxycinnamyl esters substitution rates compared with the wild type.

SUMMARY

We find that over expression of members of a grass-diverged and expanded Glade of BAHD CoA acyltransferases alter the amounts of hydroxycinnamic acids in grass cell walls. In particular, increased expression of OsAt10 increased p-CA content but decreased FA content of rice matrix polysaccharide, consistent with the tentative assignment of this enzyme as a p-coumaryl CoA transferase. Similarly, increased expression of AT15 and AT7 resulted in decreased FA. Together with the recent report that OsAT4 has p-coumaryl CoA:monolignol transferase activity, this suggests that other members of the “Mitchell clade” of CoA acyltransferases likely possess feruloyl transferase activity. Of practical importance toward improving the efficiency of biofuel production and animal feed from grass biomass, we have found that the increased OsAt10 expression increases the glucose content of and improves the digestibility of mature straw. The fact that this is an over expression effect will facilitate rapid transfer to and testing of this gene in other grass species.

Materials and Methods Acyltransferase Identification and Phylogenetic Analysis

To identify putative BAHD acyltransferases, we downloaded the hidden Markov model profile for PF02458 from the Pfam database and then searched the annotated coding sequences of diverse plant genomes to identify potential domains using HMMER v3.0 (Finn et al., 2011). We used the following genome annotation sources and versions, which were current at the time of the analysis: Arabidopsis thaliana, TAIR v10; Brachypodium dystachyon, Phytozome v7.0; Soybean, Phytozome v7.0; Medicago truncatula, Mt3.5; Rice, MSU v6.1; Physcomitrella patens, Phytozome v7.0; Poplar, Phytozome v7.0; Sorghum, Phytozome v7.0; Selaginella moellendorffii, Phytozome v7.0. To serve as a reference for phylogenetic analysis, we downloaded the sequences of 46 previously characterized BAHD enzymes from NCBI, and identified their conserved PF02458 domains as described above. e refer to these proteins as the D'Auria set (D'Auria, 2006). In addition, we randomly selected an outgroup of three PF02458-containing proteins from fungi. All phylogenetic analyses were conducted only with the Pfam domain protein sequences. If HMMER3 identified multiple segments with similarity to the PF02458 domain for a single protein, those segments were concatenated. Redundant sequences, such as from alternative splice versions of a single locus, were noted in the sequence name and only represented once in subsequent analyses.

We determined the BAHD Glade of each predicted protein via comparison to the D'Auria set. To do this, we used Clustal2 (Larkin et al., 2007) with default settings to build an alignment of the D'Auria set followed by limited manual adjustments with BioEdit. We used this alignment as a profile for alignment of each species' predicted BAHD enzymes. Based on these alignments, we omitted sequences that lack the region immediately surrounding the highly conserved active-site motif, HXXXD, and also those that lack either the H or the D, or include of an extra amino acid between them. We then used MEGA5.05 (Tamura et al., 2011) to infer and visualize neighbor joining phylogenetic trees for each species' BAHD proteins in conjunction with the D'Auria set and the outgroup sequences. Parameters were: amino acid substitutions according to the Jones-Taylor-Thorton model, gamma distribution of mutation rate among sites, distribution shape parameter of one, and gaps treated by pair-wise deletion. Five hundred bootstraps were used to identify a consensus tree for each species. Though the bootstrap values were often lower than 50%, the previously delineated BAHD clades unfailingly grouped together (D'Auria, 2006). The proteins encoded by the highly grass-expressed genes belong to Clade V. From the species BAHD trees, we identified Glade V proteins, to which, from each species for further analysis.

Clade V proteins from the diverse plant species examined were aligned, then the alignments manually edited. To achieve a high level of confidence we analyzed the relationships among the rice acyltransferase proteins of interest using Bayesian analysis, in addition to the methods described above. Using MrBayes3.1.2 (Huelsenbeck and Ronquist, 2001), the parameters for that analysis were as follows: the WAG model for amino acid substitutions (analysis with a subset of the data showed that this was the most probably fixed rate model for the data set), with a gamma rate distribution with some invariable residues. We ran the simulation for 125,000 generation until the average standard deviation of split frequencies stabilized below 0.01.

Plant Lines and Growth Conditions

We selected mutant lines for the target genes from RiceGE, which summarizes rice T-DNA flanking sequence database (An et al., 2005; Jeong et al., 2006). The initial screen was conducted on the segregating progeny of the primary transgenics, the line numbers for which are listed in Table II. Seeds from the stock center were sterilized with a 40% commercial bleach solution and germinated on a half-strength Murashige and Skoog (MS) medium containing 1.5% sucrose, 0.55 mM myo-inositol and 0.2% phytagel at 28° C. with continuous white light. After seven days, the seedlings were transplanted into topsoil and grown in a greenhouse (20-30° C., 60 to 80% relative humidity). Natural day lengths<14 hours were supplemented with artificial lighting. For genotyping, 10-20 mg leaf samples from 10-24 segregating progeny of the first generation were harvested, frozen in liquid nitrogen, and ground with a Qiagen Tissuelyser (17 Hz, 1 minute). The samples were vortexed in 200 μL DNA extraction buffer containing 100 mM Tris-HCl (pH 9.5), 1 M KCl, and 10 mM EDTA (pH 8.0), incubated at 65° C. for 30 min, diluted with 1 mL of H2O, and centrifuged for 10 min at the maximum speed. The supernatant was used as template the template for genotyping by PCR. PCR conditions were as follows: 94° C., 5 min; 35 cycles of 95° C. for 35 sec, 56° C. for 45 sec, and 72° C. for 45 sec; 72° C. for 5 minutes. Genotyping primers are described in Supplemental Table 51. We confirmed and further characterized the next two generations in selfed progeny of homozygous mutant and negative segregant, wild-type plants of line 4A-03423, which we have named OsAT10-D1. Specifically we characterized mutant progeny of 4A-03423.5, 4A-03423.12, and 4A-03423.1.9 and negative segregant progeny of 4A-03423.5 and 4A-03423.5.6. In this nomenclature, the period indicates each new generation and the numbers following the period indicate the parent plant of the analyzed progeny.

Generation of Ubi:OsAt10 Lines

We amplified a 1541 base pair fragment encoding OsAT10 (LOC_Os06g39390.1) including both the start and stop codons from Nipponbare seedling cDNA with the cloning primers listed in Supplemental Table SI. The PCR fragment was gel purified, cloned into pENTR-DTOPO (Invitrogen), and confirmed by sequencing. We then recombined the gene into the final pCAMBIA1300-Ubi-GW-Nos construct (Park et al., 2010). This binary vector contains a Gateway cassette, flanked by the maize Ubi1 promoter and the 3′-terminator of nopaline synthase from Agrobacterium tumefaciens, and the Hpt2 gene, which confers resistance to hygromycin. We used Agrobacterium tumefaciens EHA105 to transform fresh calli from the rice japonica cultivar, Kitaake, as previously described (Cheng et al., 1997). After regeneration of plantlets, plants were transferred to the greenhouse under conditions described above, and genotyped with primers for Hpt2 (Supplemental Table SI).

Quantitative RT-PCR

We measured gene expression in young leaf samples. The samples were harvested 33 days after transplanting to the greenhouse and consisted of the top recently emerged or greater-than two-thirds emerged leaf of the 2nd or 3rd tiller. We attempted to choose morphologically and developmentally similar leaves for analysis, based on leaf length and degree of emergence/expansion. Leaves were split vertically down the mid-vein and one half dried for hydroxycinnamic acid analysis, as described below. The other half was frozen in liquid nitrogen, ground to a powder and the RNA extracted with 1 mL of Trizol reagent (Invitrogen) with subsequent processing according the manufacturer's protocol. The resulting total RNA was then purified by digestion with DNaseI and cleaned up on a Nucleospin RNA II column (Macherey-Nagel) according to the manufacturer's protocol. RNA quality was checked on a 1.4% agarose gel after denaturation with glyoxal reagent (Ambion). We synthesized cDNA from 1 μg of total RNA with VILO-Superscript (Invitrogen).

We used quantitative real time PCR to measure the expression of each target gene and potential off targets. Using an established procedure for identifying control primers (Vandesompele et al., 2002), we screened primers for three highly expressed rice genes (Ubq5, eEf1α, and 18S rRNA (Jain et al., 2006)) and two moderately expressed genes (Abp and Cc55 (Jain, 2009)) for stability of expression across a set of cDNAs made from 28 rice, aerial vegetative samples collected throughout development (Supplemental Table I, LEB and PCR in prep). Based on geNORM analysis, we used primers for Ubq5 and Cc55, the two most stably expressed genes for our samples, for internal controls in the qPCR reactions. Reactions were run in a Bio-Rad CFX thermocycler, using SsoFAST EvaGreen mastermix (Bio-Rad). Reaction efficiencies were calculated with LinRegPCR, which calculates the average efficiency for each primer pair based on all the reactions using those primers per plate (Ruijter et al., 2009). Efficiency-adjusted gene expression was normalized with the geometric mean of the control primers (Vandesompele et al., 2002), using the following equation: EAt10Cq(At10)/SQRT(ECc55Cq(Cc55)×Eubq5Cq(Ubq5)), where E and Cq indicates the average reaction efficiency and cycle number at which the threshold fluorescence level was exceeded for the designated genes, respectively.

Cell Wall Analyses Preparation of Alcohol Insoluble Residue (AIR)

Due to the significant changes in cell wall content across development, we took care to harvest developmentally similar plant organs and parts for comparisons between wild-type and mutant plants in all experiments. Samples harvested for the initial screen were dried at 65° C. and samples from subsequent generations at 45° C. for 72 hours. Immature tissue was ground by two rounds of shaking at 1200 rpm with two stainless steal balls 90 sec each. Mature aerial tissue was milled with a Wiley Mill with a 5 mm screen followed by and Udy mill with a 1 mm screen. Ground tissue (5 to 500 mg) was treated with 95% ethanol (1:4 w/v) at 100° C. for 30 min. After the treatment, the supernatant was removed by centrifugation (10,000 g, 10 min) and the residue was subsequently washed three to five times with 70% ethanol and dried at −35° C. under vacuum using a centrivap. The dried powder obtained after 70% ethanol wash is designated as alcohol insoluble residue (AIR). The AIR was destarched as described by Obro et al. (2004). AIR was treated with amylase (0.3 U/10 mg biomass Termamyl, Novozymes, Bagsverd, Denmark) in 3-(N-morpholino) propanesulfonic acid (MOPS) buffer (50 mM, pH 7.0) at 85° C. for 1 h followed by amyloglucosidase (0.33 U/10 mg biomass) and pullulanase (0.04 U/10 mg biomass) in acetate buffer, 200 mM, pH 4.5 for 2 h at 50° C. Amyloglucosidase and pullulanase were purchased from Megazyme (Bray, Ireland). The reactions were stopped by adding 3 volumes of cold 95% ethanol, vortexed, and centrifuged at 10,000 g for 10 min. The residue obtained after centrifugation was washed three times with 70% ethanol and dried at 32° C. using a CentriVap Vacuum Concentrator (Labconco Corp, MO).

Analysis of Hydroxycinnamic Acids

To release esterified hydroxycinnamic acids from the cell wall, AIR (1 to 10 mg, depending on the experiment, typically 3 mg) was saponified with 500 μl of 2 N NaOH for 24 h at 25° C. with mixing at 300 rpm. For analysis of later generations, we doped reactions with an extraction standard, trans-cinnamic acid, but this improvement had not yet been developed for the initial screening. After saponification, the supernatant was acidified (pH<2) with 100 μL concentrated HCl, vortexed, and extracted three times with 300 μL ethyl acetate. The extracts were combined and evaporated to dryness using a CentriVap at 32° C. The samples were dissolved in 50% (v/v) methanol prior to HPLC analysis. Care was taken to shield the samples from light during the entire process of extraction to prevent the isomerization of hydroxycinnamates in light.

Quantification of hydroxycinnamic acids was carried out on a Dionex Ultimate 3000 high pressure liquid chromatography (HPLC) system (Thermofisher-Dionex, Sunnyvale, Calif., USA) with UV detection. Samples were separated on a reverse-phase C18 column a Synergy 4u Fusion-RP 80 Å column (250×2 mm, Phenomenex, Torrance, Calif.) with a flow of 0.3 ml min-1 and a gradient of solvent A (0.2%, v/v, TFA) and solvent B (acetonitrile) as follows: 0-5 min, 10% B isocratic; 5-25 min, 10-30% B linear; 25-40 min, 30% B isocratic; 40-45 min, 30-35% B linear; 45-46 min, 35-100% B linear; 46-51 min, 100% B isocratic; 51-53 min 100-10% B linear; 53-60 min 10% B isocratic. The column temperature was maintained at 30° C. and detection was carried out at 320 nm. Drs. J. Ralph and F. Lu kindly provided the ferulate dehydrodimers, which were treated with 2 N NaOH prior to running as standards (Ralph et al., 1994). To confirm that the species with corresponding retention times were diferulates, we also collected the two major dimer peaks from the HPLC and then their identity verified their mass by LC-MS.

Hydroxycinnamate Fractionation

To determine whether the changes in hydroxycinnamate content were associated with the matrix polysaccharide or the lignin fractions, 6 mg of destarched AIR were mixed with 600 uL of either 0.05 M trifluoroacetate (TFA) or water. Samples were incubated with shaking at 100° C. for up to 690 minutes. At each time point, a fraction of the sample was removed and frozen. Once all the samples were collected, they were thawed and treated with 2 N NaOH for 24 hrs at 25° C. followed by neutralization with concentrated HCl. (Control duplicates remained frozen during the NaOH incubation and then were treated with NaOH and HCl). trans-Cinnamic acid was doped into the samples before they were extracted three times with 300 uL of ethyl acetate. Combined extracts were dried with no heat via speed vac and resuspended in 50:50 MeOH before HPLC analysis. For quantification of sugars released by TFA, D-xylose was measured using a D-xylose test kit (Megazyme) and D-glucose was measured using a D-fructose/D-glucose (LQR) kit (Megazyme). Both kits were used essentially according to manufacturer's directions, but with reduced volumes for use with a microplate reader. Xylose and glucose supplied with the kits were used to generate standard curves for quantification.

High Performance Liquid Chromatography-Electrospray Ionization-Mass Spectrometry

HPLC separation of the 50 mM TFA-treated samples was performed using an Agilent (Santa Clara, Calif.) 1290 HPLC system equipped with a Phenomenex (Torrance, Calif.) Kinetex reversed phase column (ODS-18, 100 mm×2.1 mm, 2.6 μm particle size). Mobile phase A consisted of 5% acetonitrile and 0.1% formic acid in HPLC-grade submicron filtered water (Fisher Scientific, Pittsburgh, Pa.). Mobile phase B consisted of 0.1% formic acid in 100% acetonitrile. These mobile phase solutions were filtered and vacuum-degassed prior to use. A binary gradient at 0.3 mL/min flow rate was applied as follows: 90% solvent A and 10% solvent B from 0 to 4 min, linear gradient to 30% solvent B from 4 to 8 min, linear gradient to 50% solvent B from 8 to 9 min, 50% solvent B from 9 to 12 min, linear gradient from 12 to 13 100% solvent B, 100% solvent B from 13 to 15 min, and linear gradient to return the mobile phase to 90% solvent A and 10% solvent B from 15 to 16 min, which was maintained for an additional 5 min before the next sample was injected. The HPLC column eluent was introduced into an Agilent 6538 UHD Accurate Mass QTOF (Santa Clara, Calif.) equipped with an electrospray ionization source operated in negative ion mode. Nitrogen gas was used as a nebulizing and drying gas with a drying gas temperature of 325° C. and 10 L/min flow rate. Fragmentor voltage was 160V and capillary voltage was 3500V. Data was collected with Mass Hunter Acquisition (B.04.00, 2011) and analyzed with Mass Hunter Qualitative (B.04.00, 2011).

Monosaccharide Composition by HPAEC Destarched AIR (2-5 mg) was treated with 2 M TFA at 120° C. for 1 h. Next the hydrolysate was completely dried using a CentriVap at 32° C. Monosaccharides produced by TFA hydrolysis were then redissolved in nanopure water and analyzed by high-performance anion exchange chromatography (HPAEC) with pulsed amperometric detection on an Dionex UltimatelCS-3000 system equipped with an electrochemical detector and a 4×250 mm CarboPac PA20 column (OBro et al., 2004). The monosaccharides used as the external standards were obtained from Sigma Aldrich, USA and Alfa Aesar, Mass., USA.

Lignin Quantification Using Acetyl Bromide

Lignin was quantified via acetylbromide solubilization (Fukushima and Hatfield, 2004), followed by quantification in a 96-well plate as described. Briefly, AIR (5 mg) was incubated with 300 μl of freshly prepared acetyl bromide (25% v/v in acetic acid, Alfa Aesar, Mass., USA)) in screw-capped eppendorf tubes (VWR#16466-044) at 50° C. for 3 h in a thermomixer at 1050 rpm, with vortexing every 15 min for the last hour. After centrifuging, 100 μl of the solution was transferred to a fresh tube, followed by addition of 400 μl of 2 N NaOH and 70 μl of freshly prepared 0.5 M hydroxylamine hydrochloride. Next, 57 μL of the solution was transferred to a uv-compatible 96-well plate, followed by addition of 200 μL of glacial acetic acid. Absorption was measured at 280 nm with a BioTek SynergyHT. The lignin content in the samples was determined with an extinction coefficient of 17.75 Lg-1 cm-1 corresponding to average values for grass samples (Fukushima and Hatfield, 2004). Pathlength was determined by measuring the height of the plate.

Pyrolysis Molecular Beam Mass Spectrometry

A commercially available molecular beam mass spectrometer (MBMS) designed specifically for biomass analysis was used for pyrolysis vapor analysis (Skyes et al., 2010). Approximately 4 mg of air-dried 20 mesh biomass was introduced into the quartz pyrolysis reactor via 80 μL deactivated stainless steel Eco-Cups provided with the autosampler. Mass spectral data from m/z 30-450 were acquired on a Merlin Automation data system version 3.0 using 17 eV electron impact ionization. Lignin estimates and S:G ratios were determined by summing the intensities of peaks assigned to lignin compounds as described (Skyes et al., 2010). Several lignin peaks were omitted in the syringyl or guaiacyl summations due to individual peaks having associations with both S and G precursors (Evans and Milne, 1987).

Thermogravimetric Analysis

Thermogravimetric experiments were run using a Netzsch STA 449 F3 TG-DTA instrument. Approximately 50 mg of the ground samples were weighed and then loaded into the thermal analyzer. The samples were measured in 50 mL/min gas flow. The gas was initially He; and the temperature was held at 35° C. for 15 minutes and then increased to 800° C. at 10 K/min. The samples were then cooled to 140° C. and the gas flow was switched to 60% air in He. The samples were then again heated to 800° C. at 5 K/min and then cooled to 290° C. and the gas flow was switched back to He. The weight data reported in Supplemenatal FIG. 5B was corrected for variations in water content by normalizing to the weight at 177° C., 30 minutes into the experiment.

Enzymatic Saccharification Assay

AIR (2-5 mg) was pretreated by shaking at 30° C. in 500 μl of 100 mM Citrate buffer (pH 5.0) followed by incubation at 100° C. for 1 hour. After cooling on the bench, 1:2000 (final dilution) NS50013, which contain a cellulose cocktail, and 1:10,000 (final dilution) NS50010, which contains β-glucosidase, from the Novozymes Biomass Kit were added to the slurry. Reactions were incubated at 50° C. with shaking with periodic removal of timepoints, which were stopped by freezing. Released reducing sugars were quantified by 3,5-dinitrosalicilate (DNS) assay (Ghose, 1987).

Fungal Deconstruction and Enzymatic Assays

Pretreatment of rice straw. Prior to steam pre-treatment, wild-type and mutant rice straw were soaked in 1.2% H2SO4 overnight. Steam-based pretreatment was performed by loading the samples into an autoclave gun and treating them at 191° C. with a residence time of 2 min. Pretreated materials were then released by rapid depressurization to allow the material to explode, breaking apart the lignin and hemi-cellulose from the cellulose. The pre-treated materials were collected, filtered, washed with distilled water, and stored at 4° C. for subsequent degradation experiments using a modified Hagglund's method (Hagglund, 1951).

Rice straw degradation. The pretreated wild-type and mutant rice straw was supplemented with 100 mL of Mandel's media in 500-mL flasks (Mandels et al., 1970). Spores from Penicillium sp. YT02 were collected from agar plates with a 0.9% NaCl solution, the adjusted to a concentration of 5.0×1012 spores mL-1, and used as inoculum [10% (v/v)] for fungal degradation.

Protein content. Fungal growth was estimated by the protein content in the supernatant. Mid-log fungal cell culture suspension was collected by centrifugation (14,000×g) for 20 min at room temperature. The supernatant was collected and protein content was determined via the Bradford method.

Enzymatic activities. Total cellulase activity was determined against Whatman no. 1 filter paper (Sigma-Aldrich, St. Louis, Mo.) using the DNS method (Xiao et al. 2004). Total endoglucanase activity was determined with carboxymethylcellulose (CMC) (Claeyssens and Aerts, 1992) followed by reducing sugar measurements with DNS (Ghose, 1987). β-glucosidase activity was determined with p-nitrophenyl-β-d-glucoside and the liberation of p-nitrophenol was accompanied by absorption spectroscopy at 410 nm (Ghose, 1987). Xylanase activity was assayed as described elsewhere (Gessesse and Gashe, 1997). One international unit (IU) was defined as the enzymatic activity needed for the release of 1 mmol of sugar equivalents per unit volume per minute. To improve accuracy, activity values are expressed relative to the protein concentration in the media (IU/mg).

Saccharides. Fungal cultures were centrifuged and the supernatants analyzed for saccharide content by HPLC using an Aminex HPX-87H (Bio-Rad, Hercules, Calif., USA) organic acid column at 65° C. The mobile phase was 5 mM sulphuric acid at a flow rate of 0.5 mL min-1. A refractive index detector was used.

Example 2 Expression of OsAT10 in Switchgrass

Switchgrass plants were transformed with a pUbi:OsAT10 construct, where pUbi is the maize ubiquitin promoter. Transformation was performed using Agrobacterium-mediated transformation of calli, and several transgenic calli were selected. A number of lines were transplanted to soil and grown for 5 to 6 months in a greenhouse. Stem material was harvested from the plants and analyzed for hydroxycinnamate content. This analysis showed a decrease of ferulic acid esters from 35.7 nmol/mg biomass in the control plants to 26.4 nmol/mg in the selected transgenic lines, corresponding to a 26% decrease in ferulate esters. Coumaroyl esters showed an increase from 32.9 nmol/mg in the wild type to 64.6 nmol/mg in the transformants. Dried stem material was pretreated with hot water at 100 C for 1 hr, and subsequently subjected to saccharification with Novozymes CTec2 enzyme cocktail for 24 hrs. Released sugars were determined by dinitrosalicylate assays. Under these conditions the wild type plants released 39.9 μg sugar per mg dry biomass whereas the transformants released 56.4 μg per mg dry biomass, corresponding to a 40% increase in released sugars.

Example 3 Decreased Expression of AT5

AT5-D1 is the result of insertion of a T-DNA that includes a transcriptional enhancer cassette near the At5 locus (LOC_Os05g19910) in rice. FIGS. 25A-25B shows quantitative reverse transcriptase PCR data indicating that At5 is over expressed, unlike other loci close to the site of insertion. Previously, we reported that this line showed enhanced cell wall ferulic acid content. FIGS. 26A-26B shows that, unlike At10-over expression lines (Bartley et al. 2013), the increased ferulic acid content of AT5-D1 is not associated with the acid-labile polysaccharide cell wall, but rather fractionates with the acid-resistant, lignin and cellulose pellet. The results of expression of the AT5 and 4-coumaryl ligase (4CL) proteins in yeast show that this causes the novel accumulation of ferulate-monolignol adducts (see below), suggesting that in AT5-D1 the modification to the lignin & cellulose fractions resides on the lignin. AT5-D1 plants grow normally in the greenhouse, under most conditions, but show reduced growth under some undefined stresses (not shown). That AT5 acts as an FMT suggests that over expression of this enzyme in bioenergy crops or crop plant organs that do not normally contain ferulated lignin, can be used to introduce ester linkages into the lignin that can be easily cleaved with weak base pretreatment for subsequent saccharification and biofuel production. Although this concept was shown (Wilkerson et al, 2014). However, AT5 shows only very low sequence similarity to the AsFMT gene described in the Ralph work (18% identity, 30% similarity, FIG. 27), consistent with convergent evolution of the FMT activity in monocots and dicots, and the possibility at AT5 represents a different approach to the problem of introducing ester linkages into lignin.

Plant Lines and Growth Conditions

Plants were grown in (1:1) Turface Athletics medium:vermiculite mix supplemented with fertilizer (JACKS PROFESSIONAL LX 15-5-15 4Ca 2Mg) 3 times a week at a temperature of 85° F.-87° F. during daytime and 75° F.-77° F. during night. Natural day lengths less than 13 h were supplemented with artificial lighting.

OsAT5-D1 qRT-PCR

We measured gene expression in young leaf samples. The samples were harvested 5 weeks after transplanting to the greenhouse and consisted of the top, recently emerged or greater than two-thirds emerged leaf of the second or third tiller. We attempted to choose morphologically and developmentally similar leaves for analysis, based on leaf length and degree of emergence/expansion. Leaves were split vertically down the midvein, and one-half was dried for hydroxycinnamic acid analysis, as described below. The other one-half was frozen in liquid nitrogen, ground to a powder, and the RNA was extracted with 1 mL of Trizol reagent (Invitrogen) with subsequent processing according to the manufacturer's protocol. The resulting total RNA was then purified by digestion with DNaseI and cleaned up on a Nucleospin RNA II column (Macherey-Nagel) according to the manufacturer's protocol. RNA quality was checked on a 1.4% agarose gel after denaturation with glyoxal reagent (Ambion). We synthesized cDNA from 1 mg of total RNA with VILO-Superscript (Invitrogen).

We used quantitative real-time PCR to measure the expression of each target gene and potential off targets. Using an established procedure for identifying control primers (Vandesompele et al., 2002), we screened primers for three highly expressed rice genes (Ubq5, eEf1a, and 18S rRNA; Jain et al., 2006) and two moderately expressed genes (Abp and Cc55; Jain, 2009) for the stability of expression across a set of cDNAs made from 28 rice aerial vegetative samples collected throughout development (Supplemental Table S1; L. E. Bartley and P. C. Ronald, unpublished data). Based on geNORM analysis, we used primers for Ubq5 and Cc55, the two most stably expressed genes for our samples, for internal controls in the quantitative PCR. Reactions were run in a Bio-Rad CFX96 thermocycler using SsoFAST EvaGreen Mastermix (Bio-Rad). Reaction efficiencies were calculated with LinRegPCR, which calculates the aver-age efficiency for each primer pair based on all the reactions using those primers per plate (Ruijter et al., 2009). Efficiency-adjusted gene expression was normalized with the geometric mean of the control primers (Vandesompele et \ al. 2002) using the following equation: SQRT(E_(Cc55) ^(Cq(Cc55))×E_(Ubc5) ^(Cq(Ubq5)))/E_(goi) ^(Cq(goi)), where E and Cq indicate the average reaction efficiency and cycle number at which the threshold fluorescence level was exceeded for the designated genes, respectively, and goi indicates the experimental “gene of interest.”

OsAT5-D1 Hydroxycinnamate Fractionation

To determine whether the changes in hydroxycinnamate content were associated with the matrix polysaccharide or the lignin fractions, 6 mg of destarched AIR was mixed with 600 mL of either 0.05 M TFA or water, similar to a previously described method (Saulnier et al., 1995). Samples were incu-bated with shaking at 100° C. for up to 690 min. At each time point, a fraction of the sample was removed and frozen. Thawed samples were treated with 2 N NaOH for 24 h at 25° C. followed by neutralization with concentrated HCl. trans-Cinnamic acid was doped into the samples prior to three extractions with 300 mL of ethyl acetate. Combined extracts were dried with a CentriVap without heat and resuspended in 50:50 methanol for HPLC analysis. The multiple time points show that the reaction that liberates the matrix poly-saccharide goes approximately to completion. Longer times or higher acid concentrations caused degradation of the hydroxycinnamates.

In further experiments, AT5 and Arabidopsis thaliana 4-coumarate-CoA ligase (4CL) and AT5 were co-expressed in Saccharamycetes cerevisiae. The yeast were fed various permutations of hydroxycinnamic acids and monolignols as acyl donors and acceptors, respectively (Scheme 1). Monolignol ester conjugate formation in the yeast intracellular fraction was detected using liquid chromatography-mass spectrometry (LC/MS).

The results show that only the feruloyl adduct of monolignol ester was detected, not the monolignol ferulate conjugate. Expression of AT4/PMT in the yeast assay yielded coumaryl-ester conjugate, consistent with previous results (data not shown). This demonstrates that AT5 transfers feruloyl-CoA to monolignol moieties (FIG. 1) and that AT5 specifically used ferulic acid as acyl donor (Table 1).

ADDITIONAL REFERENCE CITED

-   Agblevor F A, Evans R J, Johnson K D (1994) Molecular-beam     mass-spectrometric analysis of lignocellulosic materials: I.     Herbaceous biomass. Journal of Analytical and Applied Pyrolysis 30:     125-144 -   Allerdings E, Ralph J, Schatz P F, Gniechwitz D, Steinhart H, Bunzel     M (2005) Isolation and structural identification of diarabinosyl     8-O-4-dehydrodiferulate from maize bran insoluble fibre.     Phytochemistry 66: 113-124 -   An G, Lee S, Kim S H, Kim S R (2005) Molecular genetics using T-DNA     in rice. Plant Cell Physiol 46: 14-22 -   Beekwilder J, Alvarez-Huerta M, Neef E, Verstappen F W, Bouwmeester     H J, Aharoni A (2004) Functional characterization of enzymes forming     volatile esters from strawberry and banana. Plant Physiol 135:     1865-1878 -   Buanafina M MdO (2009) Feruloylation in Grasses: Current and Future     Perspectives. Mol Plant 2: 861-872 -   Bunzel M, Heuermann B, Kim H, Ralph J (2008) Peroxidase-catalyzed     oligomerization of ferulic acid esters. J Agric Food Chem 56:     10368-10375 -   Bunzel M, Ralph J, Lu F, Hatfield R D, Steinhart H (2004) Lignins     and ferulate-coniferyl alcohol cross-coupling products in cereal     grains. J Agric Food Chem 52: 6496-6502 -   Carpita N C (1996) Structure and Biogenesis of the Cell Walls of     Grasses Annu Rev Plant Physiol Plant Mol Biol 47: 445-476 -   Casler M D, Jung H-J G (2006) Relationships of fibre, lignin, and     phenolics to in vitro fibre digestibility in three perennial     grasses. Animal Feed Science and Technology 125: 151-161 -   Chen X, Vega-Sanchez M, Bartley L E, Verhertbruggen Y, Chiniquy D,     Canlas P E, Fagerström A, Prak L, Christensen U, Oikawa A, Chem M,     Zuo S, Auer M, Willats W G, Harholt J, Scheller H V, Ronald P C (in     prep) The OsIRX10 glycosyltansferase is critical for xylan     biosynthesis in rice. -   Cheng X, Sardana R, Altosaar I (1997) Rice transformation by     Agrobacterium infection. In C Cunningham, A J R Porter, eds, Methods     in Biotechnology: Recombinant Proteins from Plants—Production and     Isolation of Clinically Useful Compounds, Vol 3. Humana, Totowa,     N.J., pp 1-9 -   Claeyssens M, Aerts G (1992) Characterisation of cellulolytic     activities in commercial Trichoderma reesei preparations: An     approach using small, chromogenic substrates. Bioresource Technology     39: 143-146 -   D'Auria J C (2006) Acyltransferases in plants: a good time to be     BAHD. Current Opinion in Plant Biology 9: 331-340 -   Evans R J, Milne T A (1987) Molecular characterization of the     pyrolysis of biomass. Energy & Fuels 1: 123-137 -   Faulds C B, Mandalari G, LoCurto R, Bisignano G, Waldron K W (2004)     Arabinoxylan and mono- and dimeric ferulic acid release from     brewer's grain and wheat bran by feruloyl esterases and glycosyl     hydrolases from &lt;i&gt;Humicola insolens&lt;/i&gt. Applied     Microbiology and Biotechnology 64: 644-650 -   Fincher G B (2009) Revolutionary times in our understanding of cell     wall biosynthesis and remodeling in the grasses. Plant Physiol 149:     27-37 -   Finn R D, Clements J, Eddy S R (2011) HMMER web server: interactive     sequence similarity searching. Nucleic Acids Res -   Fu C, Mielenz J R, Xiao X, Ge Y, Hamilton C Y, Rodriguez M, Chen F,     Foston M, Ragauskas A, Bouton J, Dixon R A, Wang Z-Y (2011) Genetic     manipulation of lignin reduces recalcitrance and improves ethanol     production from switchgrass. Proceedings of the National Academy of     Sciences 108: 3803-3808 -   Fu C, Xiao X, Xi Y, Ge Y, Chen F, Bouton J, Dixon R, Wang Z-Y (2011)     Downregulation of Cinnamyl Alcohol Dehydrogenase (CAD) Leads to     Improved Saccharification Efficiency in Switchgrass. BioEnergy     Research 4: 153-164 -   Fukushima R S, Hatfield R D (2004) Comparison of the Acetyl Bromide     Spectrophotometric Method with Other Analytical Lignin Methods for     Determining Lignin Concentration in Forage Samples. Journal of     Agricultural and Food Chemistry 52: 3713-3720 -   Gessesse A, Gashe B A (1997) Production of alkaline xylanase by an     alkaliphilic Bacillus sp. isolated from an alkaline soda lake.     Journal of Applied Microbiology 83: 402-406 -   Ghose T K (1987) Measurement of Cellulase Activities. Pure and     Applied Chemistry 59: 257-268 -   Grabber J H, Hatfield R D, Ralph J (1998) Diferulate cross-links     impede the enzymatic degradation of non-lignified maize walls.     Journal of the Science of Food and Agriculture 77: 193-200 -   Grabber J H, Quideau S, Ralph J (1996) p-coumaroylated syringyl     units in maize lignin: Implications for [beta]-ether cleavage by     thioacidolysis. Phytochemistry 43: 1189-1194 -   Grabber J H, Ralph J, Hatfield RD (1998) Ferulate Cross-Links Limit     the Enzymatic Degradation of Synthetically Lignified Primary Walls     of Maize. Journal of Agricultural and Food Chemistry 46: 2609-2614 -   Hägglund E (1951). In E Hagglund, ed, Chemistry of Wood. Academic,     New York, N.Y., pp 374-379 -   Hatfield R, Marita J, Frost K, Grabber J, Ralph J, Lu F, Kim     H (2009) Grass lignin acylation: p-coumaroyl transferase activity     and cell wall characteristics of C3 and C4 grasses. Planta 229:     1253-1267 -   He X, Zhang J (2005) Rapid Subfunctionalization Accompanied by     Prolonged and Substantial Neofunctionalization in Duplicate Gene     Evolution. Genetics 169: 1157-1164 -   Hoffmann L, Maury Sp, Martz F B, Geoffroy P, Legrand M (2003)     Purification, Cloning, and Properties of an Acyltransferase     Controlling Shikimate and Quinate Ester Intermediates in     Phenylpropanoid Metabolism. Journal of Biological Chemistry 278:     95-103 -   Hu W J, Harding S A, Lung J, Popko J L, Ralph J, Stokke D D, Tsai C     J, Chiang V L (1999) Repression of lignin biosynthesis promotes     cellulose accumulation and growth in transgenic trees. Nat     Biotechnol 17: 808-812 -   Huelsenbeck J P, Ronquist F (2001) MRBAYES: Bayesian inference of     phylogenetic trees. Bioinformatics 17: 754-755 -   Humphrey T V, Bonetta D T, Goring DR (2007) Sentinels at the wall:     cell wall receptors and sensors. New Phytologist 176: 7-21 -   Ishii T (1991) Isolation and characterization of a diferuloyl     arabinoxylan hexasaccharide from bamboo shoot cell-walls.     Carbohydrate Research 219: 15-22 -   Ishii T, Hiroi T, Thomas J R (1990) Feruloylated xyloglucan and     p-coumaroyl arabinoxylan oligosaccharides from bamboo shoot     cell-walls. Phytochemistry 29: 1999-2003 -   Jain M (2009) Genome-wide identification of novel internal control     genes for normalization of gene expression during various stages of     development in rice. Plant Science 176: 702-706 -   Jain M, Nijhawan A, Tyagi A K, Khurana J P (2006) Validation of     housekeeping genes as internal control for studying gene expression     in rice by quantitative real-time PCR. Biochem Biophys Res Commun     345: 646-651 -   Jeong D H, An S, Park S, Kang H G, Park G G, Kim S R, Sim J, Kim Y     O, Kim M K, Kim J, Shin M, Jung M, An G (2006) Generation of a     flanking sequence-tag database for activation-tagging lines in     japonica rice. Plant J 45: 123-132 -   Jung H G, Phillips R L (2010) Putative Seedling Ferulate Ester (sfe)     Maize Mutant: Morphology, Biomass Yield, And Stover Cell Wall     Composition And Rumen Degradability. Crop Sci. 50: 403-418 -   Jung K H, An G, Ronald P C (2008) Towards a better bowl of rice:     assigning function to tens of thousands of rice genes. Nat Rev Genet     9: 91-101 -   Kellogg E A (2001) Evolutionary History of the Grasses. Plant     Physiol. 125: 1198-1205 -   Kovacs K, Macrelli S, Szakacs G, Zacchi G (2009) Enzymatic     hydrolysis of steam-pretreated lignocellulosic materials with     Trichoderma atroviride enzymes produced in-house. Biotechnology for     Biofuels 2 -   Lal R (2005) World crop residues production and implications of its     use as a biofuel. Environment International 31: 575-584 -   Lam T B-T, Iiyama K, Stone B A (2003) Hot alkali-labile linkages in     the walls of the forage grass Phalaris aquatica and Lolium perenne     and their relation to in vitro wall digestibility. Phytochemistry     64: 603-607 -   Lanoue A, Burlat V, Henkes G J, Koch I, Schurr U, Rose US (2009) De     novo biosynthesis of defense root exudates in response to Fusarium     attack in barley. New Phytol -   Larkin M A, Blackshields G, Brown N P, Chenna R, McGettigan P A,     McWilliam H, Valentin F, Wallace I M, Wilm A, Lopez R, Thompson J D,     Gibson T J, Higgins D G (2007) Clustal W and Clustal X version 2.0.     Bioinformatics 23: 2947-2948 -   Lee D, Meyer K, Chapple C, Douglas C J (1997) Antisense suppression     of 4-coumarate:coenzyme A ligase activity in Arabidopsis leads to     altered lignin subunit composition. Plant Cell 9: 1985-1998 -   Lynd L R, Laser M S, Bransby D, Dale B E, Davison B, Hamilton R,     Himmel M, Keller M, McMillan J D, Sheehan J, Wyman C E (2008) How     biotech can transform biofuels. Nat Biotechnol 26: 169-172 -   MacAdam J W, Grabber J H (2002) Relationship of growth cessation     with the formation of diferulate cross-links and p-coumaroylated     lignins in tall fescue leaf blades. Planta 215: 785-793 -   Mandels M, Andreotti R, Roche C (1970) Measurement of saccharifying     cellulase. Biotechnology and Bioengineering Symposium 6: 21-33 -   Mitchell R A, Dupree P, Shewry P R (2007) A novel bioinformatics     approach identifies candidate genes for the synthesis and     feruloylation of arabinoxylan. Plant Physiol 144: 43-53 -   Molina I, Beisson-Li Y, Beisson F, Ohlrogge J B, Pollard M (2009)     Identification of an Arabidopsis Feruloyl-CoA Transferase Required     for Suberin Synthesis. Plant Physiol -   Mueller-Harvey I, Hartley R D, Harris P J, Curzon E H (1986) Linkage     of p-coumaroyl and feruloyl groups to cell-wall polysaccharides of     barley straw. Carbohydrate Research 148: 71-85 -   Obel N, Nuemetzler L, Pauly M (2006) Hemicelluloses and cell     expansion. In J-P Verbelen, K Vissenberg, eds, Plant Cell     Monographs: The Expanding Cell, Vol 5. Springer, Berlin, pp 57-88 -   Obel N, Porchia A C, Scheller H V (2002) Dynamic changes in cell     wall polysaccharides during wheat seedling development.     Phytochemistry 60: 603-610 -   OBro J, Harholt J, Scheller H V, Orfila C (2004) Rhamnogalacturonan     I in Solanum tuberosum tubers contains complex arabinogalactan     structures. Phytochemistry 65: 1429-1438 -   Park C J, Bart R, Chem M, Canlas P E, Bai W, Ronald P C (2010)     Overexpression of the endoplasmic reticulum chaperone BiP3 regulates     XA21-mediated innate immunity in rice. PLoS ONE 5: e9262 -   Piston F, Uauy C, Fu L, Langston J, Labavitch J, Dubcovsky J (2010)     Down-regulation of four putative arabinoxylan feruloyl transferase     genes from family PF02458 reduces ester-linked ferulate content in     rice cell walls. Planta 231: 677-691 -   Ralph J (2010) Hydroxycinnamates in lignification. Phytochemistry     Reviews 9: 65-83 -   Ralph J, Quideau S, Grabber J H, Hatfield R D (1994) Identification     and synthesis of new ferulic acid dehydrodimers present in grass     cell walls. Journal of the Chemical Society, Perkin Transactions 1:     3485-3498 -   Rautengarten C, Ebert B, Ouellet M, Nafisi M, Baidoo E E, Benke P,     Stranne M, Mukhopadhyay A, Keasling J D, Sakuragi Y, Scheller H     V (2012) Arabidopsis Deficient in Cutin Ferulate encodes a     transferase required for feruloylation of omega-hydroxy fatty acids     in cutin polyester. Plant Physiol 158: 654-665 -   Ruijter J M, Ramakers C, Hoogaars W M, Karlen Y, Bakker O, van den     Hoff M J, Moorman A F (2009) Amplification efficiency: linking     baseline and bias in the analysis of quantitative PCR data. Nucleic     Acids Res 37: e45 -   Santiago R, Reid L M, Amason J T, Zhu X, Martinez N, Malvar R     A (2007) Phenolics in Maize Genotypes Differing in Susceptibility to     Gibberella Stalk Rot (Fusarium graminearum Schwabe). Journal of     Agricultural and Food Chemistry 55: 5186-5193 -   Santiago R, Sandoya G, Butrón A, Barros J, Malvar R A (2008) Changes     in Phenolic Concentrations during Recurrent Selection for Resistance     to the Mediterranean Corn Borer (Sesamia nonagrioides Lef.). Journal     of Agricultural and Food Chemistry 56: 8017-8022 -   Sasayama D, Azuma T, Itoh K (2011) Involvement of cell wall-bound     phenolic acids in decrease in cell wall susceptibility to expansins     during the cessation of rapid growth in internodes of floating rice.     J Plant Physiol 168: 121-127 -   Scheller H V, Ulvskov P (2010) Hemicelluloses. Annu Rev Plant Biol     61: 263-289 -   Skyes R, Yung M, Novaes E, Kirst M, Peter G, Davis M (2010)     High-Throughput Screening of Plant Cell-Wall Composition Using     Pyrolysis Molecular Beam Mass Spectroscopy. In JR Mielenz, ed,     Biofuels: Methods and Protocols, Vol 581. Humana Press, pp 169-183 -   Takahama U, Oniki T (1994) Effects of Ascorbate on the Oxidation of     Derivatives of Hydroxycinnamic Acid and the Mechanism of Oxidation     of Sinapic Acid by Cell Wall-Bound Peroxidases. Plant and Cell     Physiology 35: 593-600 -   Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011)     MEGA5: molecular evolutionary genetics analysis using maximum     likelihood, evolutionary distance, and maximum parsimony methods.     Molecular biology and evolution 28: 2731-2739 -   Tuominen L, Johnson V, Tsai C-J (2011) Differential Phylogenetic     Expansions in BAHD Acyltransferases Across Five Angiosperm Taxa and     Evidence of Divergent Expression Among Populus Paralogues. BMC     Genomics 12: 236 -   Unno H, Ichimaida F, Suzuki H, Takahashi S, Tanaka Y, Saito A,     Nishino T, Kusunoki M, Nakayama T (2007) Structural and mutational     studies of anthocyanin malonyltransferases establish the features of     BAHD enzyme catalysis. J Biol Chem 282: 15812-15822 -   US-DOE (2011) U.S. Billion-Ton Update: Biomass Supply for a     Bioenergy and Bioproducts Industry. In R D Perlack, B J Stokes, eds.     Oak Ridge National Labs, Oak Ridge, Tenn., p 227 -   Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe     A, Speleman F (2002) Accurate normalization of real-time     quantitative RT-PCR data by geometric averaging of multiple internal     control genes. Genome Biol 3: RESEARCH0034 -   Vogel J (2008) Unique aspects of the grass cell wall. Curr Opin     Plant Biol 11: 301-307 -   Walker K, Long R, Croteau R (2002) The final acylation step in taxol     biosynthesis: cloning of the taxoid C13-side-chain     N-benzoyltransferase from Taxus. Proc Natl Acad Sci USA 99:     9166-9171 -   Withers S, Lu F, Kim H, Zhu Y, Ralph J, Wilkerson C G (2012)     Identification of grass-specific enzyme that acylates monolignols     with p-coumarate. J Biol Chem 287: 8347-8355 -   Wu A M, Rihouey C, Seveno M, Hornblad E, Singh S K, Matsunaga T,     Ishii T, Lerouge P, Marchant A (2009) The Arabidopsis IRX10 and     IRX10-LIKE glycosyltransferases are critical for glucuronoxylan     biosynthesis during secondary cell wall formation. Plant J 57:     718-731 -   Zhou J Z, Xue K, Xie J P, Deng Y, Wu L Y, Cheng X H, Fei S F, Deng S     P, He Z L, Van Nostrand J D, Luo Y Q (2012) Microbial mediation of     carbon-cycle feedbacks to climate warming. Nature Climate Change 2:     106-110 -   Bartley, et al., (2013). “Overexpression of a Band Acyltransferase,     Osat10, Alters Rice Cell Wall Hydroxycinnamic Acid Content and     Saccharification.” Plant Physiol 161(4): 1615-1633. -   Wilkerson, et al., (2014). “Monolignol Ferulate Transferase     Introduces Chemically Labile Linkages into the Lignin Backbone.”     Science 344(6179): 90-93.

It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, accession numbers, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.

ILLUSTRATIVE SEQUENCES AT10 Acyltransferase cDNA Sequence LOC_OS06G39390.1 SEQ ID NO: 1 ATGGGCGTCTTCGCCGTCACCAAGGTGTCCGAGGGCCCCGTCCGGCCGTC CGCAGCGACGCCGTCGGAGACGCTGCCGCTCGCCTGGGTCGACCGCTACC CGACGCACCGCGGCCTCGTCGAGTCCGTGCACATCTACCTCCGCCGCGAC GACGCCGCCGTCGAGGCGCCGTGCGCCGACGGCGGCGTCATCGTCGAGGG AAAGAAGAAGAATAATAAGCCGGCGGCGGCGGTGGTGCGCGGCGCGCTGG CGGACGCGCTGGTGCACTACTACCCGTTCGCGGGGCGGATCGTGGAGGAC GAGCGGTCGCCGGGGCGGCCTGCCGTGCTGTGCTCCGGCGAGGGCGTCTA CTTCGTGGAGGCCGCCGCCAACTGCACCCTCGCCGACGTCAACCACCTGG AGCGGCCGCTGCTGCTGTCCAAGGAGGACCTCGTGCCGTGCCCGACGCCG GAGCAGTGGCCCGTCGAGCCGCACAACAGCCTCGCCATGATCCAGGTGAC GACGTTCACCTGCGGCGGCTTCGTGATCGGGCTGCGCACCAACCACGCGG TGGCGGACGGCACCGGCGCCGCCCAGTTCATGAACGCCGTCGGCGACCTC GCCCGCGGCCTCCCGGAGCCGCGGGTGAAGCCGATCTGGGCGCGCGACCG CTTCCCGGACCCGGACATCAAGCCCGGCCCGCTGCCGGAGCTCCCCGTGC TGCCGCTCCAGTACATCGCCTTCGACTTCCCCGCCGCCTACCTCGGCAAG CTCAAGGCGCAGTACGCCGCCACCGCCGGCGCCAGCAAGATCTGCTCCGC CTTCGACATCGTCATCGCCAAGCTCTGGCAGTGCCGGACGCGCGCCATCG CCGCCGACCCCGCCGCGGCCGTCAAGCTCTGCTTCTTCGCCAGCGCCCGC CAGGTGCTCGGCCTGGAGACCGGCTACTGGGGCAACGCCATCTTCCCGGT GAAGGTGTCCGCGGCGGCGGGGGAGGTGGCGGCGTCGTCGGTGATCGAGC TCGTCGGCGTGGTCCGGGAGGCGAAGCGGCGGATGGCCGGCGAGTGCCTG CGCTGGGCGGAGGGGCGCACCGGCGGCGCCGACCCGTTCCAGATGACGTT CGACTACGAGTCCGTGTACGTGTCGGACTGGAGCAAGCTCGGGTTCAACG ACGTCGACTACGGGTACGGCGCGCCGTCGGCGGCGGGGCCGCTGGTGAAC TGCGACCTCATCTCGTCGGTGATCGTCATGCGGGCGCCGGCGCCGCTCGC CGGCACGCGGCTGCTGGCGAGCTGCGTCACCAAGGAGCACGCCGACGACT TCGCCGCCAGGATGAGGGAGGATCTCGTCTAA AT10 Acyltransferase Protein Sequence LOC_Os06g39390.1 (encoded by SEQ ID NO: 1) SEQ ID NO: 2 MGVFAVTKVSEGPVRPSAATPSETLPLAWVDRYPTHRGLVESVHIYLRRD DAAVEAPCADGGVIVEGKKKNNKPAAAVVRGALADALVHYYPFAGRIVED ERSPGRPAVLCSGEGVYFVEAAANCTLADVNHLERPLLLSKEDLVPCPTP EQWPVEPHNSLAMIQVTTFTCGGFVIGLRTNHAVADGTGAAQFMNAVGDL ARGLPEPRVKPIWARDRFPDPDIKPGPLPELPVLPLQYIAFDFPAAYLGK LKAQYAATAGASKICSAFDIVIAKLWQCRTRAIAADPAAAVKLCFFASAR QVLGLETGYWGNAIFPVKVSAAAGEVAASSVIELVGVVREAKRRMAGECL RWAEGRTGGADPFQMTFDYESVYVSDWSKLGFNDVDYGYGAPSAAGPLVN CDLISSVIVMRAPAPLAGTRLLASCVTKEHADDFAARMREDLV* AT15 Acyltransferase cDNA Sequence LOC_OS10G01920.1 SEQ ID NO: 3 ATGAGTATTGTGGTGAGCAAGTCAGCGCCGGTGGTCGTCCGGCCATCGGA GCCGGCCACATCGACGGCCGACAAGATCCTTCTGTCAACTTTGGACAAGC CTGTTGCCACGATACCAGTGACCGTGCTACTTGCGTTCGACCACCCCATC CATGACGCCACCGCGGAGACCATCAAGACGGCTCTCGCTCAATCACTCGT CCACTACTATCCTATCGCCGGCCGCATTTCCTGCGACAATGACGACGGCG GCCATTTCTACATCGACTGCACCGGCGAGGATCTCGGGGTCACGTTCGTG GCCGCGTCCGCCAACTGCACCATGGAGGAGCTCATGTGTCTCGTCGACGA CCAGGCTCCCGACGACGAGACAGCGGTGGTGCAGCAGCTCGCCTTCAACT GCACGCCCGACGACCTTCATCACCGTCTGCTGTGGGTGCAGGTCACCACT CTCAACTGTGGAGGCTTCGTCGTCGGGGTGACATGGAGCCATGGCGTGGC TGACGGTCCCGGCATAGCACAGTTCATACAAGCCGTCGGCGAGCTCGCCC GTGGCCTGCCATCGCCGTCCGTCGTCCCGGTCAGGTTGGACGACAAGATC GCAACCCAAGCCGTACCTCCCTTCACCATGGCCGTTCATCGCTTCATATC CGGCCTCAAGCCAGTATCAAACCTCGACGTACGCAACGTCACCGTCTCAT CTAGCCTTATCAACCACATCATCGTCGGAGCTCGTCGTCGTGCCACCGTG TTCGAGGCGGTCGCCGCCGTGCTCTGGCAGTGCCGTACACGGGTGGTGAT GACGGATCCTGAGGCCCCCGCCGTGCTGCTCTTCGCGGTGAACGCACGCA AGTACCTCGGCGCCAAGGACGGCTACTACGGATGCTGCACCGCCATGCAC ATGGCCGTGTCCAAGTCCGGCACGGTGGCCAACGGCGACATCATGAAGTT GGTCGGCATCATACGCCGCGCCAAGGAGCAGATACCGGAGCAGCTGAAGG CAGACGACGGCGAGATGATGCTACGGACGATGGTAGGGGAGAAGCAGGTG AATGGATACGAGAGCCTGCTCTACTTGACATCCTGGCGAAACATCGGGTT CGAGGACGTCGATTTCGGCAGCGGGAAGACGGCGAGGGTGATGACCTACC CGCCGAGGATGCTGTCCATGATGCCCAGGATTGCGCCCATCTGCTTCATG CTCAAGGCCACAGAGGAAGGGGTCAGGGTCATGTCAGACTGTGTTACGGC CTGACCACGCGATGCCTTCTATCAAGAAATAGCCAAGCTCAAAGCCACCA CCTGA AS15 Acyltransferase Protein Sequence LOC_OS10G01920.1 (encoded by SEQ ID NO: 3) SEQ ID NO: 4 MSIVVSKSAPVVVRPSEPATSTADKILLSTLDKPVATIPVTVLLAFDHPI HDATAETIKTALAQSLVHYYPIAGRISCDNDDGGHFYIDCTGEDLGVTFV AASANCTMEELMCLVDDQAPDDETAVVQQLAFNCTPDDLHHRLLWVQVTT LNCGGFVVGVTWSHGVADGPGIAQFIQAVGELARGLPSPSVVPVRLDDKI ATQAVPPFTMAVHRFISGLKPVSNLDVRNVTVSSSLINHIIVGARRRATV FEAVAAVLWQCRTRVVMTDPEAPAVLLFAVNARKYLGAKDGYYGCCTAMH MAVSKSGTVANGDIMKLVGIIRRAKEQIPEQLKADDGEMMLRTMVGEKQV NGYESLLYLTSWRNIGFEDVDFGSGKTARVMTYPPRMLSMMPRIAPICFM LKATEEGVRVMSDCVTADHADAFYQEIAKLKATT* AT7 Acyltransferase cDNA Sequence LOC_Os05g08640.1 SEQ ID NO: 5 ATGGCGGCGGCGGCGCCGGACAAGGCGGTGGAGCGGCTGTCCCAGAAGCT GGTGCACCCGTCGTCCCCCACGCCGTCGGCCCCGCTCCGCCTCTCCTGGC TCGACCGCTACCCCACCCAGATGGCGCTCATCGAGTCGCTCCACGTCTTC AAGCCCGACCCGGCGAGGGACGCCGCGGGGCAGGGGCTCGCCCCCGCGCG CGCCATCGAGACGGCCCTCGCGAGAGCCCTCGTCGAGTACTACCCGCTCG CCGGGAGGCTCGCCGTCTCCCGGGACTCCGGCGAGCTCCAGGTGGATTGC TGCGGCGGCGCCGGCGGCCATGGCGGGGTGTGGTTCATCGAGGCGGCTGT CCCGTGCCGGCTCGAGGACGTGGATTACCTCGAGTACCCTCTCGCCATCT CCAAGGACGAGCTGCTCCCCCACCCGCGCCCCCGCCCCACCCGCGACGAG GAAGACAAGCTCATCCTGCTCGTCCAGGTGACGACGTTCGCGTGCGGCGG GTTCGTGGTGGGGTTCAGGTTCAGCCACGCGGTGGCGGACGGCCCGGGGG CGGCGCAGTTCATGGGCGCGGTCGGCGAGCTCGCCCGCGGCGGCGAGCGC ATCACGGTGGCCCCGTCGTGGGGGCGCGACGCGGTGCCCGACCCGGCCGG CGCCATGGTCGGCGCCCTCCCGGAGCCGGCCGGCGCGTCCCGCCTCGAGT ACCTCGCCATCGACATCTCCGCCGACTACATCAACCACTTCAAGTCCCAG TTCGCGGCGGCCACCGGCGGCGCCCGCTGCTCCGCCTTCGAGGTGCTCAT CGCCAAGGCATGGCAGAGCCGCACCCGCGCCGCCGCGTTCGACCCCTCGA CGCCGATCAACCTCTCCTTCGCCATGAACGCCCGGCCGCTCCTCCTCCCG CGCGGCGGCGCCGGGTTCTACGGCAACTGCTACTACATCATGCGGGTGGC CTCCACCGCCGGGAGGGTGGCGACGGCGAGCGTCACCGACGTGGTGAGGA TGATCCGGGAGGGGAAGAAGCGGCTCCCGTCGGAGTTCGCGCGGTGGGCC GCCGGAGAGATGGCCGGAGTCGACCCGTACCAGATCACCTCCGACTACCG GACGCTGCTGGTCTCCGACTGGACGCGGCTGGGCTTCGCCGAGGTGGACT ACGGGTGGGGCCCACCGGGCCACGTCGTGCCGCTCACGAACCTGGACTAC ATCGCCACGTGTATCCTCGTCAAGCCCTGGGCCCACAAACCAGGGGCACG GCTCATCACCCAGTGCGTCACACCCGACCGCGTCACCGCCTTCCACGACG CCATGGTGGACATCAACTAA AT7 Protein Sequence LOC_Os05g08640.1 (encoded by SEQ ID NO: 5) SEQ ID NO: 6 MAAAAPDKAVERLSQKLVHPSSPTPSAPLRLSWLDRYPTQMALIESLHVF KPDPARDAAGQGLAPARAIETALARALVEYYPLAGRLAVSRDSGELQVDC CGGAGGHGGVWFIEAAVPCRLEDVDYLEYPLAISKDELLPHPRPRPTRDE EDKLILLVQVTTFACGGFVVGFRFSHAVADGPGAAQFMGAVGELARGGER ITVAPSWGRDAVPDPAGAMVGALPEPAGASRLEYLAIDISADYINHFKSQ FAAATGGARCSAFEVLIAKAWQSRTRAAAFDPSTPINLSFAMNARPLLLP RGGAGFYGNCYYIMRVASTAGRVATASVTDVVRMIREGKKRLPSEFARWA AGEMAGVDPYQITSDYRTLLVSDWTRLGFAEVDYGWGPPGHVVPLTNLDY IATCILVKPWAHKPGARLITQCVTPDRVTAFHDAMVDIN* AT5 cDNA sequence LOC_Os05g19910.1 SEQ ID NO: 7 ATGGTCGCTGTCACCGTGATGAGGAAGTCCCGGAACTTCGTCGGGCCGTC TCCTCCGACGCCGCCGGCCGAGATCACGACGACGCTCGAGCTGTCGTCCA TCGACCGCGTGCCCGGGCTGCGCCACAACGTGCGGTCCCTGCACGTGTTC CGCCGCCACAAGAACAGCGGGCCCGTCGTCGACGGTGATAGCAGGAGGCC GGCCGCCGTGATCCGCGCGGCGCTCGCCCGGGCGCTGGCGGACTACCCGG CGTTCGCCGGCCGATTCGTCGGCTCCCTGCTGGCCGGCGACGCCTGCGTC GCGTGCACCGGCGAGGGCGCGTGGTTCGTGGAGGCAGCCGCGGACTGCAG CCTCGACGACGTGAACGGCCTCGAGTACCCGCTCATGATCTCCGAGGAGG AGCTGCTGCCTGCCCCCGAGGACGGCGTCGACCCTACCAGTATTCCAGTC ATGATGCAGGTGACTGAATTCACTTGTGGAGGATTTATCTTGGGCCTTGT GGCAGTCCACACCCTTGCTGATGGACTTGGAGCAGCACAATTCATCACTG CAGTAGCTGAATTGGCCCGTGGCATGGACAAGCTCAGGGTGGCTCCCGTG TGGGATCGCTCGCTGATACCGAACCCACCTAAGCTCCCTCCTGGGCCACC ACCATCGTTCCAGTCCTTTGGTTTTCAGCATTTCTCCACAGATGTCACCT CTGACCGTATAGCTCACGTGAAGGCTGAGTACTTCCAGACCTTTGGCCAG TATTGTTCCACCTTTGATGTTGCTACTGCTAAGGTTTGGCAGGCCAGGAC ACGGGCCGTCGGGTACAAACCGGAGATCCAGGTCCATGTGTGTTTCTTTG CAAACACGCGTCACCTGCTCACGCAGGTTCTCCCAAAAGATGGGGGCTAC TATGGCAACTGCTTTTATCCAGTGACTGTGACAGCAATAGCTGAGGATGT TGCCACCAAAGAGTTGCTTGATGTGATCAAGATAATTCGGGATGGAAAGG CGAGGCTCCCCATGGAGTTTGCAAAGTGGGCTTCAGGGGATGTGAAAGTT GATCCCTACGCATTGACATTTGAACACAATGTGCTTTTTGTGTCTGATTG GACGAGGTTAGGATTCTTCGAGGTAGACTATGGGTGGGGTACACCTAATC ACATCATACCATTCACTTATGCAGACTACATGGCAGTCGCAGTGCTTGGT GCTCCACCAATGCCAAAGAAAGGGACCCGGATTATGACACAGTGTGTGGA GAACAAGTGTATCAAGGAGTTCCAAGATGAGATGAAGGCCTTCATATAA AT5 polypeptide sequence LOC_Os05g19910.1 (encoded by SEQ ID NO: 7) SEQ ID NO: 8 MVAVTVMRKSRNFVGPSPPTPPAEITTTLELSSIDRVPGLRHNVRSLHVF RRHKNSGPVVDGDSRRPAAVIRAALARALADYPAFAGRFVGSLLAGDACV ACTGEGAWFVEAAADCSLDDVNGLEYPLMISEEELLPAPEDGVDPTSIPV MMQVTEFTCGGFILGLVAVHTLADGLGAAQFITAVAELARGMDKLRVAPV WDRSLIPNPPKLPPGPPPSFQSFGFQHFSTDVTSDRIAHVKAEYFQTFGQ YCSTFDVATAKVWQARTRAVGYKPEIQVHVCFFANTRHLLTQVLPKDGGY YGNCFYPVTVTAIAEDVATKELLDVIKIIRDGKARLPMEFAKWASGDVKV DPYALTFEHNVLFVSDWTRLGFFEVDYGWGTPNHIIPFTYADYMAVAVLG APPMPKKGTRIMTQCVENKCIKEFQDEMKAFI*

TABLE I BAHD CoA acyltransferases encoded in some sequenced plant genomes. # putative BAND Clade V: proteins: Total (# AT AT Total (# Perfect Perfect Clade Clade Species HXXXD)^(a) HXXXD) ^(a,b) i^(c) ii^(c) Physcomitrella patens  17 (16)  8 (7) 0 0 Selaginella moellendorffii  74 (65) 19 (19) 0 0 Oryza sativa 122 (117) 61 (60) 10 10 Sorghum biocolor  89 (85) 49 (48) 8 4 Brachypodium dystachion  83 (78) 38 (38) 12 4 Arabidopsis thaliana  64 (61) 25 (25) 1 0 Populus tricocarpa 125 (121) 25 (24) 0 0 Medicago truncatula  89 (83) 30 (27) 1 0 Glycine max 142 (135) 70 (65) 2 0 ^(a)Consists of nonredundant predicted protein sequences identified via HMMER3.0 based on PFAM v. 25 and that contain the region surrounding the conserved active site motif, HXXXD, though proteins with single amino acid variations in either the H or D are included. The number in parentheses is the number with the strict HXXXD motif. See Results for justification. ^(b) As in D'Auria 2006. ^(c)Acyltransferase (AT) protein clades delineated in FIGS. 1A-1B and Supplemental FIG. 1.

TABLE II Summary of the rice acyltransferase mutant analysis. Gene Locus ID EST Mutant Line Line Class Insert Immature leaf and sheath cell wall Name^(a) (LOC_)^(b) Count^(c) ID (PFG_) cv^(d) (putative) Detected hydroxycinnamic acid phenotype^(e) OsAt1 Os01g42880 86 3A-13924 DJ AT^(f) No ND^(g) OsAt2 Os01g42870 25 NA^(h) OsAt3 Os05g04584 49 3A-02783 DJ AT No ND OsAt4 Os01g18744 50 3A-02300 DJ Insert/AT^(i) Yes, no ND homozygotes 3A-09297 DJ Insert/AT No ND OsAt5 Os05g19910 17 2A-20021^(j) DJ AT Yes Leaf and sheath: increase in FA:p-CA ratio 1C-03624 HY Insert^(k) No ND OsAt6 Os01g08380 76 1C-06931 HY Insert No ND 3A-08459 DJ AT No ND 2D-40810 HY AT Yes None OsAt7 Os05g08640 15 2A-40095 HY Insert/AT Yes Sheath: decrease FA OsAt8 Os06g39470 5 NA OsAt9 Os01g09010 200 NA OsAt10 Os06g39390 41 4A-03423^(l) DJ AT Yes Leaf: decrease FA, increase p-CA Sheath: decrease FA, increase p-CA OsAt11 Os04g11810 0 NA OsAt12 Os04g09590 0 3A-16373 DJ AT Yes None 2D-41616 HY AT Yes None OsAt13 Os10g01930 0 2D-10182 DJ Insert/AT Yes, no ND homozygotes OsAt14 Os10g02000 9 NA OsAt15 Os10g01920 0 1B-00523 DJ AT Yes Leaf: decrease FA OsAt16 Os10g01800 0 2D-40243 DJ AT Yes None OsAt17 Os10g03360 0 NA OsAt18 Os10g03390 1 4A-04176 DJ AT Yes None OsAt19 Os04g09260 7 NA OsAt20 Os06g48560 0 NA Totals 20 17 11 confirmed, 4 phenotypes (for 11 2 no genes) homozyg. for insert ^(a) Oryza sativa (Os) acyltransferase (At) gene names were assigned arbitrarily based on an early phylogenic analysis, that has since been revised. ^(b)Annotation MSUv6 ^(c)Sum of ESTs from all organs/stages from rice Sanger EST data available through 2009. ^(d)DJ and HW indicate O. sativa var. japonica cv. Dongjin and cv. Hwayoung, respectively ^(e)For homozygous mutants relative to negative segregant wild-type siblings. CA signifies para-coumaric acid. FA signifies ferulic acid. A change in FA:CA ratio is only mentioned when a phenotype in neither FA nor CA alone appear to change. ^(f)AT signifies a putative activation tagged line in the T-DNA insert possesses transcription activation sequences. ^(g)ND signifies not determined. ^(h)NA signifies that no rice activation lines were available at the inception of the study. ^(i)Insert/AT signifies that the T-DNA possesses transcription activation sequences and is inserted within, or <300 base pairs away from, the gene. ^(j)OsAT5-D1 ^(k)Insert signifies that the T-DNA is inserted within, or <300 base pairs away from, the gene. ^(l)OsAT10-D1

TABLE III Lignin Amounts and S:G Ratios from AIR after 2N NaOH extraction for greenhouse grown mutant and wildtype plants. Standardize Parental ABSL ^(a) d Lignin ^(c) Line Genotype Material (% mass) S/G ratio ^(b) (% mass) WT^(d) 4A-03423.1 mature 5.5 ± 0.5 0.67 ± 0.01 5.7 ± 0.2 straw AT10-D1 4A-03423.5 mature 5.5 ± 0.5 0.75 ± 0.11 5.5 ± 0.1 straw AT10-D1 4A-03423.12 mature 5.7 ± 0.6 ND ^(e) ND straw WT 4A-03423 leaf sheath ND 0.39 ± 0.05 5.9 ± 0.1 AT10-D1 4A-03423 leaf sheath ND 0.36 ± 0.13 5.5 ± 0.7 WT 4A-03423 leaf blade ND 0.52 ± 0.13 3.4 ± 0.1 AT10-D1 4A-03423 leaf blade ND 0.52 ± 0.09 3.4 ± 0.3 ^(a) Acetylbromide soluble lignin expressed in terms of mg/mg for pools of straw, measured in triplicate, or 2 to 3 individual bioreplicates, measured in duplicate. Errors are standard deviations. ^(b) Average ± standard deviation of singlicate measurements of 2 to 3 plants for the earlier generation, and two technical replicates of pools of 12 plants for the later generation samples, as determined by py-MBMS. ^(c) As determined via py-MBMS and calibrated for each type of rice sample (i.e., straw, leaf, sheath) based on the ABSL data. ^(d)negative segregant, wild type. ^(e) ND = not determined

SUPPLEMENTAL TABLE I Primers used in examples A. Primers used for genotyping (SEQ ID NOS: 43-75). primer pair for 5′ 5′ primer 3′ 3′ primer T-DNA::plant Line primer name sequence (5->3) primer name sequence (5->3) junction L0.5 TTGGGGATCCTCTAGAGTCG AG iLl TCCGAAACTATCAGTGTCTA GCT NGUS1 AACGCTGATCAATTCCACAG 1A-19542 Pam1-1F GTGGTGGAAAGTTGTGATCG Pam1-1R_15LB CAGGGCATGTTTAGTT Pam1-1R_15LB/ GGTG L0.5 5A-00394 Pam1-3F CTCAACCGCCATCATGTTAC Pam1-3R_15LB GTTCCTATCACATCGG Pam1-3R_15LB/ ATGT L0.5 1B-00523 Pam1-8F_15LB GATGGGACAGTCTCTAGTCA Pam1-8R GTAGTACGCGAGATCC Pam1-8F_15LB/ GTAT L0.5 3A-02300 Pam1-12F_15RB TGCAGCCTCGACGACGTGA Pam1-12R TGATCCGTTAGCGCGT Pam1-12F_ GTT 15RB/NGUS1 2A-20021 Pam1-13F TGACTGAAGGTCGAGAACGA Pam1-13R_15LB GTTACATGATGCCTTG Pam1-13R_15LB/ TCAAG L0.5 2D-40818 Pam1-15F GCAGCTCAACTCCTGAAAATC Pam1-15R_72RB GCCAGCTGATCTGAAG Pam1-15R_72RB/ CAG NGUS1 4A-03423 Pam1-16F_15LB CCAGAGGGAGTACTTCCGT Paml-16R GCGAGATGGCTATACG Pam1-16F_15LB/ TGAG L0.5 3A-13924 Pam1-17F CCATCTTAGAGATGGGAGCA Pam1-17R_15RB CGTCCTTGGATCTGGG Pam1-17R_15RB/ TCA NGUS1 2D-10182 Pam1-19F CAGATGAGCTTATAGCTAGT Pam1-19R_72LB GACTTGCTCACCACAA Pam1-19R_72LB/ TGCT iL1 4A-04176 Pam1-22F_15RB GTGGTTAGAACCTCCCTAGA Pam1-22R CTCATGGATCGGATGC Pam1-22F_15RB/ TCGA NGUS1 2A-40095 Pam1-25F_15RB TCACGAACCTGGACTACATC Pam1-25R ACCATCTACCTGTACC Pam1-25F_15RB/ CTCA NGUS1 1C-03624 Pam1-26F_07RB GTGACGGAGGCAGTGATGA Pam1-26R GCTTAAGTGCAGCCCA Pam1-26F_07RB/ AACT NGUS1 3A-16373 Pam1-28F CAAGAGGGCATAAGTGAACT Pam1-28R_15LB CATCGGAAGGTGATTC Pam1-28R_15LB/ CACA L0.5 2D-41616 Pam1-29F CAGTTGCAGACCACTGAGAA Pam1-29R_72LB CTTGATTCTCGAGTTGA Pam1-29R_72LB/ AAGT iL1 Ubi:: Hyg-3 TCCACTATCGGCGAGTACTT hyg 4 CACTGGCAAACTGTGAT OsAt10 CATACAC GGACGAC B. RT-qPCR primers(SEQ ID NOS: 76-99) ID 5′ primer name 5′ primer sequence 3′ primer name 3′ primer sequence purpose LOC_ Os01g08380_F1 AGGCCGGGAGGATGGGTGGATT Os01g08380_ ACCACGCTCCACCCACG experimental Os01g08380 R1 AGCTT LOC_ os01g09010_ cacctgctgaagctggacag os01g09010_ tccatcaccgacgacga experimental Os01g09010 832F 929R cagca LOC_ 04g09260-2-f GGAAGCACGTCGGAGCCAAG 04g09260-2-r CGACATGATGCAGTTGC experimental Os04g09260 CGTAG LOC_ os05g08640_ AAACCAGGGGCACGGCTCAT os05g08640_ TTGATGTCCACCATGGC experimental Os05g08640 F4qPCR R4qPCR GTCGT LOC_ os05g19910_ catcactgcagtagctgaat os05g19910_ gcttaggtgggttcggt experimental Os05g19910 543F tgg 634R atcagc LOC_ Os06g39370_F1 TGCCTTCTAGAAATCTGAAG Os06g39370_R1 TTGCTGTACAAACTCGAA experimental Os06g39370 CGTAT CTCTGC LOC_ Os06g39380_F1 ACAGAAAAACCACGGCCTAA Os06939380_R1 CTCTTTTCACTCCCACCC experimental Os06939380 TAGA TTGTCT LOC_ 06g39390-RT2- GACCCGTTCCAGATGACGTT 06g39390-RT2- GATGAGGTCGCAGTTCAC experimental Os06g39390 5′ 3′ CA LOC_ Os06g39400_F1 GCGCATGGAAGGGCAAAAAC Os06g39400_R1 CTGCTCCAGAAAAAGCTCG experimental Os06939400 AGC ATCGGT LOC_ os06g39470_ agtacccgctcatggtggac os06g39470_ aactgcgtgacctggacaa experimental Os06g39470 359F 467R LOC_ CC55 R1-5′ AAGGAGAAAGCCGAACAACG CC55 RT1-3′ TCCTCAAGTTTCTTCCTG control Os04935910 TAGGC LOC_ UBQ5 RT 1-5′ ACCACTTCGACCGCCACTACT UBQ5 RT1-3′ ACGCCTAAGCCTGCTGGTT control Os01g22490 C. Cloning primers (SEQ ID NOS: 100-101) gene 5′ targeted primer name 5′ primer sequence 3′ primer name 3′ primer sequence LOC_ Os06g39390- CACCAGCAGCAGCAGCAGCAG Os06g39390- TACCACGCATGTCACAAAG Os06g39390 for-2 CAGC rev-stop2 CACGG

SUPPLEMENTAL TABLE II Average ± standard deviation of sugar composition of the media during the course of Penicillium sp. YT02 incubation with OsAT10-D1 and negative segregant, wild type. N = 5. Glucose Xylose Arabinose Time WT Mut Δ WT Mut Δ WT Mut Δ (hrs) (mg/mL) (mg/mL) % (mg/mL) (mg/mL) % (mg/mL) (mg/mL) % 12 0.42 ± 0.01 0.42 ± 0.02 0 0.17 ± 0.03 0.32 ± 0.04 88 0.05 ± 0.02 0.05 ± 0 0.01 24 1.4 ± 0.1 1.5 ± 0.4 3 0.7 ± 0.3 1.4 ± 0.5 106 0.14 ± 0.05 0.24 ± 71 0.01 36 2.1 ± 0.1 2.3 ± 0.2 9 0.8 ± 0.2 1.8 ± 0.4 116 0.27 ± 0.03 0.40 ± 48 0.01 48 2.7 ± 0.1 4.4 ± 0.3 65 1.2 ± 0.5 2.3 ± 0.2 95 0.5 ± 0.2 0.39 ± −19 0.02 60 3.5 ± 0.1 4.7 ± 0.3 35 1.7 ± 0.3 2.7 ± 0.2 64 0.6 ± 0.2 0.63 ± 5 0.02 72 3.4 ± 0.1 6.1 ± 0.2 82 1.8 ± 0.1 3.7 ± 0.4 102 0.5 ± 0.5 0.60 ± 25 0.03 84 3.3 ± 0.1 4.8 ± 0.1 47 2.0 ± 0.2 2.9 ± 0.2 45 0.6 ± 0.3 0.80 ± 35 0.05 96 1.8 ± 0.1 3.4 ± 0.2 97 1.4 ± 0.1 2.5 ± 0.2 84 0.5 ± 0.2 0.64 ± 28 0.03 120 1.1 ± 0.1 1.4 ± 0.1 28 1.6 ± 0.1 2.4 ± 0.2 48 0.5 ± 0.2 0.48 ± 7 0.03 Avg 46 82 25 Galactose Mannose Cellobiose Time WT Mut Δ WT Mut Δ WT Mut Δ (hrs) (mg/mL) (mg/mL) % (mg/mL) (mg/mL) % (mg/mL) (mg/mL) % 12 0.02 ± 0.02 ± 0 0.04 ± 0.04 ± 0 0.20 ± 0.09 ± 0.01 −55 0.01 0.01 0.01 0.01 0.01 24 0.11 ± 0.04 ± −62 0.18 ± 0.16 ± −9 0.38 ± 0.36 ± 0.02 −4 0.02 0.01 0.02 0.01 0.01 36 0.09 ± 0.10 ± 11 0.14 ± 0.20 ± 48 0.54 ± 0.35 ± 0.02 −35 0.03 0.01 0.06 0.03 0.01 48 0.18 ± 0.16 ± −13 0.42 ± 0.23 ± −44 0.70 ± 0.55 ± 0.04 −22 0.06 0.01 0.04 0.04 0.01 60 0.15 ± 0.27 ± 80 0.38 ± 0.45 ± 20 0.85 ± 0.81 ± 0.05 −5 0.02 0.03 0.03 0.03 0.02 72 0.16 ± 0.12 ± −25 0.24 ± 0.48 ± 100 0.95 ± 1.2 ± 0.2 27 0.04 0.02 0.04 0.02 0.01 84 0.15 ± 0.40 ± 170 0.15 ± 0.30 ± 103 0.73 ± 0.80 ± 0.05 10 0.02 0.03 0.03 0.02 0.03 96 0.65 ± 0.24 ± −63 0.10 ± 0.40 ± 300 0.60 ± 0.80 ± 0.04 34 0.01 0.01 0.02 0.02 0.02 120 0.36 ± 0.03 ± −17 0.36 ± 0.30 ± −17 0.37 ± 0.78 ± 0.02 110 0.01 0.02 0.05 0.01 0.03 Avg 10 63 14 

What is claimed is:
 1. A method of engineering a plant to decrease the ferulic acid content in the plant, the method comprising: introducing an expression cassette into the plant, wherein the expression cassette comprises a polynucleotide encoding an AT10, AT7, or AT15 acyltransferase wherein the acyltransferase has at least 70% identity to a sequence selected from SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6, and culturing the plant under conditions in which the acyltransferase is expressed.
 2. The method of claim 1, wherein the polynucleotide is operably linked to a promoter endogenous to the plant.
 3. The method of claim 1, wherein the expression cassette comprises a promoter to which the polynucleotide is operably linked.
 4. The method of claim 3, wherein the promoter is a tissue-specific promoter.
 5. The method of claim 4, wherein the promoter drives expression in cell wall.
 6. The method of claim 5, wherein the polynucleotide has at least 70% identity to SEQ ID NO:1, SEQ ID NO:3, or SEQ ID NO:5.
 7. A method of engineering a plant to increase the ferulic acid content in the plant, the method comprising: introducing an expression cassette into the plant, wherein the expression cassette comprises a polynucleotide encoding an AT5 acyltransferase wherein the acyltransferase has at least 70% identity to SEQ ID NO:8, and culturing the plant under conditions in which the acyltransferase is expressed.
 8. The method of claim 7, wherein the polynucleotide is operably linked to a promoter endogenous to the plant.
 9. The method of claim 7, wherein the expression cassette comprises a promoter to which the polynucleotide is operably linked.
 10. The method of claim 9, wherein the promoter is a tissue-specific promoter.
 11. The method of claim 7, wherein the polynucleotide has at least 85% identity to SEQ ID NO:8.
 12. The method of claim 1, wherein the plant is a grass plant.
 13. The method of claim 12, wherein the grass plant is rice, corn, switchgrass, sorghum, millet, miscanthus, sugarcane, alfalfa, wheat, soy, rye, barley, turfgrass, hemp, bamboo, rape, sunflower, or brachypodium.
 14. A plant engineered by the method of claim 1, or a progeny of the plant.
 15. A plant cell comprising a polynucleotide encoding an AT10, AT15, AT7, or AT5 operably linked to a heterologous promoter; or a plant comprising a heterologous polynucleotide encoding an AT10, AT15, AT7, or AT5 protein.
 16. Biomass comprising the plant or a part of the plant of claim
 14. 17. A method of obtaining an increased amount of soluble sugars from a plant in a saccharification reaction, the method comprising: subjecting the plant of claim 14 to a saccharification reaction, thereby increasing the amount of soluble sugars that can be obtained from the plant as compared to a wild-type plant.
 18. A plant engineered by the method of claim 7, or a progeny of the plant.
 19. Biomass comprising the plant or a part of the plant of claim
 18. 20. A method of obtaining an increased amount of soluble sugars from a plant in a saccharification reaction, the method comprising: subjecting the plant of claim 18 to a saccharification reaction, thereby increasing the amount of soluble sugars that can be obtained from the plant as compared to a wild-type plant. 